Annotations: 8SYI

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	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
C	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	PF10385	RNA polymerase beta subunit external 1 domain (RNA_pol_Rpb2_45)	RNA polymerase beta subunit external 1 domain	RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between ...	RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region [1].	Domain
C	PF04560	RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7)	RNA polymerase Rpb2, domain 7	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 p ...	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 comprised of the structural domains anchor and clamp [1]. The clamp region (C-terminal) contains a zinc-binding motif [1]. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription [1].	Domain
C	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	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
C	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	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	PF04983	RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)	RNA polymerase Rpb1, 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). This domain, domain 3, represents the pore doma ...	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 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].	Domain
D	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
E [auth Z]	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
E [auth Z]	PF04983	RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)	RNA polymerase Rpb1, 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). This domain, domain 3, represents the pore doma ...	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 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].	Domain
E [auth Z]	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
F [auth E]	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family
G	PF02357	Transcription termination factor nusG (NusG)	Transcription termination factor nusG	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	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	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 anatomical structure intracellular anatomical structure cytoplasm 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
C	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	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	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	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	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	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 Z]	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	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	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 E]	DNA-directed RNA polymerase subunit omega	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	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	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
G	Transcription termination/antitermination protein NusG	-	negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization negative regulation of metabolic process primary metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination positive regulation of biological process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of gene expression negative regulation of biosynthetic process cellular process transcription elongation by RNA polymerase II transcription elongation-coupled chromatin remodeling DNA-templated transcription elongation transcription by RNA polymerase II chromatin organization chromatin remodeling regulation of DNA-templated transcription elongation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
H [auth N]	DNA (37-MER)	-	-	-
I [auth R]	RNA (5'-R(PUPUPCPAPAPAPGPCPGPGPAPGPAPGPGPUP*A)-3')	-	-	-
J [auth T]	DNA (37-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
A, B	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
A, B	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
A, B	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
A, B	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
A, B	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
C	IPR007642	RNA polymerase Rpb2, domain 2	Domain
C	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
C	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
C	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
C	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
C	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
C	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
C	IPR007645	RNA polymerase Rpb2, domain 3	Domain
C	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
C	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
C	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
C	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
C	IPR007641	RNA polymerase Rpb2, domain 7	Domain
D	IPR012755	DNA-directed RNA polymerase, subunit gamma	Family
D	IPR007066	RNA polymerase Rpb1, domain 3	Domain
D	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
D	IPR034678	DNA-directed RNA polymerase subunit RpoC1	Family
D	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
D	IPR000722	RNA polymerase, alpha subunit	Domain
D	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
D	IPR006592	RNA polymerase, N-terminal	Domain
D	IPR007080	RNA polymerase Rpb1, domain 1	Domain
E [auth Z]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
E [auth Z]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
E [auth Z]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
E [auth Z]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
E [auth Z]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
E [auth Z]	IPR012756	DNA-directed RNA polymerase, subunit beta''	Family
E [auth Z]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
F [auth E]	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
F [auth E]	IPR003716	DNA-directed RNA polymerase, omega subunit	Family
F [auth E]	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
G	IPR043425	NusG-like	Family
G	IPR001062	Transcription antitermination protein, NusG	Family
G	IPR036735	NusG, N-terminal domain superfamily	Homologous Superfamily
G	IPR014722	Large ribosomal subunit protein uL2, domain 2	Homologous Superfamily
G	IPR015869	Transcription antitermination protein, NusG, bacteria, conserved site	Conserved Site
G	IPR008991	Translation protein SH3-like domain superfamily	Homologous Superfamily
G	IPR047050	NusG, N-terminal	Domain
G	IPR005824	KOW	Domain
G	IPR006645	NusG-like, N-terminal	Domain