8W9Z

The cryo-EM structure of the Nicotiana tabacum PEP-PAP

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth a]	PF01193	RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L)	RNA polymerase Rpb3/Rpb11 dimerisation domain	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.	Domain
A, B [auth a]	PF01000	RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac)	RNA polymerase Rpb3/RpoA insert domain	Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal	Domain
A, B [auth a]	PF03118	Bacterial RNA polymerase, alpha chain C terminal domain (RNA_pol_A_CTD)	Bacterial RNA polymerase, alpha chain C terminal domain	The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. T ...	The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal [2].	Domain
K [auth I]	PF00294	pfkB family carbohydrate kinase (PfkB)	pfkB family carbohydrate kinase	This family includes a variety of carbohydrate and pyrimidine kinases.	Domain
M [auth J]	PF00856	SET domain (SET)	SET domain	-	Family
M [auth J]	PF09273	Rubisco LSMT substrate-binding (Rubis-subs-bind)	Rubisco LSMT substrate-binding	Members of this family adopt a multihelical structure, with an irregular array of long and short alpha-helices. They allow binding of the protein to substrate, such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco ho ...	Members of this family adopt a multihelical structure, with an irregular array of long and short alpha-helices. They allow binding of the protein to substrate, such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco holoenzyme complex [1].	Domain
O [auth L]	PF00081	Iron/manganese superoxide dismutases, alpha-hairpin domain (Sod_Fe_N)	Iron/manganese superoxide dismutases, alpha-hairpin domain	superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytopla ...	superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. N-terminal domain is a long alpha antiparallel hairpin. A small fragment of YTRE_LEPBI matches well - sequencing error?	Domain
O [auth L]	PF02777	Iron/manganese superoxide dismutases, C-terminal domain (Sod_Fe_C)	Iron/manganese superoxide dismutases, C-terminal domain	superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplas ...	superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. C-terminal domain is a mixed alpha/beta fold.	Domain
P [auth M], Q [auth m]	PF00085	Thioredoxin (Thioredoxin)	Thioredoxin	Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. Some members with only the active site are not separated from the noise.	Domain
R [auth N]	PF08245	Mur ligase middle domain (Mur_ligase_M)	Mur ligase middle domain	-	Domain
R [auth N]	PF01225	Mur ligase family, catalytic domain (Mur_ligase)	Mur ligase family, catalytic domain	This family contains a number of related ligase enzymes which have EC numbers 6.3.2.*. This family includes: MurC (Swiss:P17952), MurD (Swiss:P14900), MurE (Swiss:P22188), MurF (Swiss:P11880), Mpl (Swiss:P37773) and FolC (Swiss:P08192). MurC, MurD, ...	This family contains a number of related ligase enzymes which have EC numbers 6.3.2.*. This family includes: MurC (Swiss:P17952), MurD (Swiss:P14900), MurE (Swiss:P22188), MurF (Swiss:P11880), Mpl (Swiss:P37773) and FolC (Swiss:P08192). MurC, MurD, Mure and MurF catalyse consecutive steps in the synthesis of peptidoglycan. Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide. The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine. The peptide moiety is synthesised by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine. This family also includes Folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate.	Domain
R [auth N]	PF02875	Mur ligase, glutamate ligase domain (Mur_ligase_C)	Mur ligase, glutamate ligase domain	This entry contains a number of related ligase enzymes which have EC numbers 6.3.2.* which includes: MurC (Swiss:P17952), MurD (Swiss:P14900), MurE (Swiss:P22188), MurF (Swiss:P11880), Mpl (Swiss:P37773) and FolC (Swiss:P08192). MurC, MurD, MurE and ...	This entry contains a number of related ligase enzymes which have EC numbers 6.3.2.* which includes: MurC (Swiss:P17952), MurD (Swiss:P14900), MurE (Swiss:P22188), MurF (Swiss:P11880), Mpl (Swiss:P37773) and FolC (Swiss:P08192). MurC, MurD, MurE and MurF catalyse consecutive steps in the synthesis of peptidoglycan. Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide. The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine. The peptide moiety is synthesised by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine [1,3,4]. This entry also includes folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate and cyanophycin synthetase that catalyses the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin) [2].	Domain
T [auth P]	PF05899	EutQ-like cupin domain (Cupin_3)	EutQ-like cupin domain	This entry represents the cupin domain, with a conserved jelly roll-like beta-barrel fold capable of homodimerisation found in bacteria, plant and fungi. It is present in EutQ family from the eut operon, involved in ethanolamine degradation. EutQ is ...	This entry represents the cupin domain, with a conserved jelly roll-like beta-barrel fold capable of homodimerisation found in bacteria, plant and fungi. It is present in EutQ family from the eut operon, involved in ethanolamine degradation. EutQ is essential during anoxic growth and has acetate kinase activity [1]. The cupin domain from EutQ does not possess the His residues responsible for metal coordination in other classes of cupins [2]. This domain is also found in (S)-ureidoglycine aminohydrolase (UGlyAH) from E.coli, which is involved in the anaerobic nitrogen utilisation via the assimilation of allantoin. It catalyses the deamination of allantoin to produce S-ureidoglycolate and ammonia from S-ureidoglycine [3,4].	Domain
C [auth B]	PF04561	RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2)	RNA polymerase Rpb2, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA po ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [1]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).	Domain
C [auth B]	PF04565	RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3)	RNA polymerase Rpb2, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site [1].	Domain
C [auth B]	PF00562	RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6)	RNA polymerase Rpb2, domain 6	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain [1]. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion[1]. This domain is also involved in binding to Rpb1 and Rpb3 [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).	Domain
D [auth C]	PF00623	RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)	RNA polymerase Rpb1, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2].	Domain
D [auth C]	PF05000	RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)	RNA polymerase Rpb1, domain 4	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel do ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2].	Domain
D [auth C]	PF04998	RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)	RNA polymerase Rpb1, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontin ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2].	Domain
D [auth C]	PF04997	RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1)	RNA polymerase Rpb1, domain 1	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp do ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2].	Domain
G [auth E]	PF01535	PPR repeat (PPR)	PPR repeat	-	Repeat
G [auth E]	PF13812	Pentatricopeptide repeat domain (PPR_3)	Pentatricopeptide repeat domain	-	Repeat
G [auth E]	PF17177	Pentacotripeptide-repeat region of PRORP (PPR_long)	Pentacotripeptide-repeat region of PRORP	-	Repeat
G [auth E]	PF13041	PPR repeat family (PPR_2)	PPR repeat family	-	Repeat
I [auth G]	PF00081	Iron/manganese superoxide dismutases, alpha-hairpin domain (Sod_Fe_N)	Iron/manganese superoxide dismutases, alpha-hairpin domain	superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytopla ...	superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. N-terminal domain is a long alpha antiparallel hairpin. A small fragment of YTRE_LEPBI matches well - sequencing error?	Domain
I [auth G]	PF02777	Iron/manganese superoxide dismutases, C-terminal domain (Sod_Fe_C)	Iron/manganese superoxide dismutases, C-terminal domain	superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplas ...	superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. C-terminal domain is a mixed alpha/beta fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth a]	DNA-directed RNA polymerase subunit alpha	DNA binding binding organic cyclic compound binding nucleic acid binding protein binding protein dimerization activity DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity DNA binding binding organic cyclic compound binding nucleic acid binding protein binding protein dimerization activity DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle chloroplast transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle chloroplast transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
K [auth I]	Fructokinase-like 1, chloroplastic	kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	plastid transcription cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process plastid transcription cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process cellular component organization organelle organization plastid organization chloroplast organization cellular component organization or biogenesis	membrane-bounded organelle intracellular anatomical structure plastid plastid nucleoid nucleoid cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle chloroplast nucleoid plastid stroma organelle intracellular non-membrane-bounded organelle chloroplast stroma cytoplasm membrane-bounded organelle intracellular anatomical structure plastid plastid nucleoid nucleoid cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle chloroplast nucleoid plastid stroma organelle intracellular non-membrane-bounded organelle chloroplast stroma cytoplasm non-membrane-bounded organelle chloroplast
L [auth i]	Fructokinase-like 2, chloroplastic	-	plastid transcription cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process plastid transcription cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process cellular component organization organelle organization plastid organization etioplast organization cellular component organization or biogenesis chloroplast organization	membrane-bounded organelle intracellular anatomical structure plastid plastid nucleoid nucleoid cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle chloroplast nucleoid plastid stroma organelle intracellular non-membrane-bounded organelle chloroplast stroma cytoplasm membrane-bounded organelle intracellular anatomical structure plastid plastid nucleoid nucleoid cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle chloroplast nucleoid plastid stroma organelle intracellular non-membrane-bounded organelle chloroplast stroma cytoplasm non-membrane-bounded organelle chloroplast
M [auth J]	Protein PLASTID TRANSCRIPTIONALLY ACTIVE 14-like isoform X2	transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity	methylation metabolic process	-
N [auth K]	PAP8(pTAC6)	-	-	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex plastid transferase complex cellular anatomical entity intracellular membrane-bounded organelle plastid-encoded plastid RNA polymerase complex transferase complex, transferring phosphorus-containing groups intracellular organelle organelle RNA polymerase complex DNA-directed RNA polymerase complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex plastid transferase complex cellular anatomical entity intracellular membrane-bounded organelle plastid-encoded plastid RNA polymerase complex transferase complex, transferring phosphorus-containing groups intracellular organelle organelle RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm intracellular protein-containing complex
O [auth L]	superoxide dismutase	cation binding ion binding binding metal ion binding small molecule binding superoxide dismutase activity oxidoreductase activity, acting on superoxide radicals as acceptor oxidoreductase activity antioxidant activity catalytic activity	-	membrane-bounded organelle intracellular anatomical structure plastid plastid nucleoid nucleoid cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle chloroplast nucleoid plastid stroma organelle intracellular non-membrane-bounded organelle chloroplast stroma cytoplasm membrane-bounded organelle intracellular anatomical structure plastid plastid nucleoid nucleoid cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle chloroplast nucleoid plastid stroma organelle intracellular non-membrane-bounded organelle chloroplast stroma cytoplasm non-membrane-bounded organelle chloroplast
P [auth M], Q [auth m]	Thioredoxin-like protein CITRX1, chloroplastic	oxidoreductase activity, acting on a sulfur group of donors disulfide oxidoreductase activity oxidoreductase activity catalytic activity catalytic activity, acting on a protein protein-disulfide reductase activity	cell redox homeostasis cellular homeostasis homeostatic process cellular component organization organelle organization plastid organization cellular process cellular component organization or biogenesis	membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle
R [auth N]	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase-like	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding acid-amino acid ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity	developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis cellular process cell division biosynthetic process developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis cellular process cell division biosynthetic process metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity
S [auth O]	Protein PLASTID TRANSCRIPTIONALLY ACTIVE 7-like isoform X1	-	plastid transcription cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process plastid transcription cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex plastid transferase complex cellular anatomical entity intracellular membrane-bounded organelle plastid-encoded plastid RNA polymerase complex transferase complex, transferring phosphorus-containing groups intracellular organelle organelle RNA polymerase complex DNA-directed RNA polymerase complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex plastid transferase complex cellular anatomical entity intracellular membrane-bounded organelle plastid-encoded plastid RNA polymerase complex transferase complex, transferring phosphorus-containing groups intracellular organelle organelle RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm intracellular protein-containing complex
T [auth P]	PAP13(pTAC18)	-	-	-
C [auth B]	DNA-directed RNA polymerase subunit beta	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups ribonucleoside binding DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle chloroplast transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle chloroplast transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
D [auth C]	DNA-directed RNA polymerase subunit gamma	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups transition metal ion binding zinc ion binding	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle chloroplast transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle chloroplast transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
E [auth c]	DNA-directed RNA polymerase subunit beta''	DNA binding binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid DNA binding binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle chloroplast transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle chloroplast transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
F [auth D]	PAP1(pTAC3)	-	-	-
G [auth E]	Pentatricopeptide repeat-containing protein At1g74850, chloroplastic-like	-	plastid transcription cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process plastid transcription cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle chloroplast
H [auth F]	Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10-like	RNA binding binding organic cyclic compound binding nucleic acid binding	-	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex plastid transferase complex cellular anatomical entity intracellular membrane-bounded organelle plastid-encoded plastid RNA polymerase complex transferase complex, transferring phosphorus-containing groups intracellular organelle organelle RNA polymerase complex DNA-directed RNA polymerase complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex plastid transferase complex cellular anatomical entity intracellular membrane-bounded organelle plastid-encoded plastid RNA polymerase complex transferase complex, transferring phosphorus-containing groups intracellular organelle organelle RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm intracellular protein-containing complex
I [auth G]	superoxide dismutase	cation binding ion binding binding metal ion binding small molecule binding superoxide dismutase activity oxidoreductase activity, acting on superoxide radicals as acceptor oxidoreductase activity antioxidant activity catalytic activity	-	-
J [auth H]	Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12-like	-	response to light stimulus response to stimulus response to radiation response to abiotic stimulus plastid transcription cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process response to light stimulus response to stimulus response to radiation response to abiotic stimulus plastid transcription cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process cellular response to stimulus positive regulation of cell communication cellular response to red or far red light regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process regulation of response to red or far red light regulation of signal transduction response to red or far red light cell communication cellular response to environmental stimulus positive regulation of response to stimulus positive regulation of red or far-red light signaling pathway cellular response to light stimulus signal transduction positive regulation of cellular process regulation of biological process regulation of signaling red or far-red light signaling pathway biological regulation cellular response to radiation regulation of response to stimulus regulation of cell communication cellular response to abiotic stimulus regulation of red or far-red light signaling pathway positive regulation of signaling positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of nucleobase-containing compound metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of cellular biosynthetic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle chloroplast nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth a]	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
A, B [auth a]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
A, B [auth a]	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
A, B [auth a]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
A, B [auth a]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
A, B [auth a]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
K [auth I]	IPR011611	Carbohydrate kinase PfkB	Domain
K [auth I]	IPR002173	Carbohydrate/purine kinase, PfkB, conserved site	Conserved Site
K [auth I]	IPR029056	Ribokinase-like	Homologous Superfamily
K [auth I]	IPR050306	PfkB Carbohydrate Kinase	Family
L [auth i]	IPR011611	Carbohydrate kinase PfkB	Domain
L [auth i]	IPR029056	Ribokinase-like	Homologous Superfamily
L [auth i]	IPR050306	PfkB Carbohydrate Kinase	Family
M [auth J]	IPR050600	SETD3/SETD6 methyltransferase	Family
M [auth J]	IPR036464	Rubisco LSMT, substrate-binding domain superfamily	Homologous Superfamily
M [auth J]	IPR046341	SET domain superfamily	Homologous Superfamily
M [auth J]	IPR015353	Rubisco LSMT, substrate-binding domain	Domain
M [auth J]	IPR001214	SET domain	Domain
N [auth K]	IPR044710	PLASTID TRANSCRIPTIONALLY ACTIVE protein 6	Family
O [auth L]	IPR036324	Manganese/iron superoxide dismutase, N-terminal domain superfamily	Homologous Superfamily
O [auth L]	IPR001189	Manganese/iron superoxide dismutase	Family
O [auth L]	IPR019833	Manganese/iron superoxide dismutase, binding site	Binding Site
O [auth L]	IPR019832	Manganese/iron superoxide dismutase, C-terminal	Domain
O [auth L]	IPR019831	Manganese/iron superoxide dismutase, N-terminal	Domain
O [auth L]	IPR036314	Manganese/iron superoxide dismutase, C-terminal domain superfamily	Homologous Superfamily
P [auth M], Q [auth m]	IPR044182	Thioredoxin-like protein CITRX, chloroplastic	Family
P [auth M], Q [auth m]	IPR013766	Thioredoxin domain	Domain
P [auth M], Q [auth m]	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
R [auth N]	IPR004101	Mur ligase, C-terminal	Domain
R [auth N]	IPR035911	MurE/MurF, N-terminal	Homologous Superfamily
R [auth N]	IPR036565	Mur-like, catalytic domain superfamily	Homologous Superfamily
R [auth N]	IPR000713	Mur ligase, N-terminal catalytic domain	Domain
R [auth N]	IPR036615	Mur ligase, C-terminal domain superfamily	Homologous Superfamily
R [auth N]	IPR013221	Mur ligase, central	Domain
R [auth N]	IPR005761	UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase	Family
S [auth O]	IPR038958	Protein plastid transcriptionally active 7	Family
T [auth P]	IPR011051	RmlC-like cupin domain superfamily	Homologous Superfamily
T [auth P]	IPR008579	(S)-ureidoglycine aminohydrolase, cupin domain	Domain
T [auth P]	IPR014710	RmlC-like jelly roll fold	Homologous Superfamily
C [auth B]	IPR007642	RNA polymerase Rpb2, domain 2	Domain
C [auth B]	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
C [auth B]	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
C [auth B]	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
C [auth B]	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
C [auth B]	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
C [auth B]	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
C [auth B]	IPR007645	RNA polymerase Rpb2, domain 3	Domain
C [auth B]	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
C [auth B]	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
C [auth B]	IPR007641	RNA polymerase Rpb2, domain 7	Domain
D [auth C]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
D [auth C]	IPR034678	DNA-directed RNA polymerase subunit RpoC1	Family
D [auth C]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
D [auth C]	IPR000722	RNA polymerase, alpha subunit	Domain
D [auth C]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
D [auth C]	IPR006592	RNA polymerase, N-terminal	Domain
D [auth C]	IPR007080	RNA polymerase Rpb1, domain 1	Domain
E [auth c]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
E [auth c]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
E [auth c]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
E [auth c]	IPR050254	DNA-directed RNA polymerase, subunit beta'', eukaryote	Family
E [auth c]	IPR012756	DNA-directed RNA polymerase, subunit beta''	Family
E [auth c]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
F [auth D]	IPR003034	SAP domain	Domain
F [auth D]	IPR036361	SAP domain superfamily	Homologous Superfamily
F [auth D]	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
F [auth D]	IPR002885	Pentatricopeptide repeat	Repeat
G [auth E]	IPR002625	Smr domain	Domain
G [auth E]	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
G [auth E]	IPR002885	Pentatricopeptide repeat	Repeat
G [auth E]	IPR033443	PROP1-like, PPR domain	Domain
H [auth F]	IPR003029	S1 domain	Domain
H [auth F]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
H [auth F]	IPR044967	Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10	Family
I [auth G]	IPR036324	Manganese/iron superoxide dismutase, N-terminal domain superfamily	Homologous Superfamily
I [auth G]	IPR001189	Manganese/iron superoxide dismutase	Family
I [auth G]	IPR019833	Manganese/iron superoxide dismutase, binding site	Binding Site
I [auth G]	IPR019832	Manganese/iron superoxide dismutase, C-terminal	Domain
I [auth G]	IPR019831	Manganese/iron superoxide dismutase, N-terminal	Domain
I [auth G]	IPR036314	Manganese/iron superoxide dismutase, C-terminal domain superfamily	Homologous Superfamily
J [auth H]	IPR034581	Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12	Family