8DH4

T7 RNA polymerase elongation complex with unnatural base dPa-DsTP pair

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth B]	RPOL_N_1	e8dh4B2	A: alpha arrays	X: HTH	H: HTH	T: HTH in T7 RNA polymerase	F: RPOL_N_1	ECOD (1.6)
A [auth B]	RNA_pol_2nd	e8dh4B1	A: alpha arrays	X: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	H: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	T: helical bundle in Bacillus stearothermophilus-like DNA polymerase I	F: RNA_pol_2nd	ECOD (1.6)
A [auth B]	RNA_pol_1st	e8dh4B5	A: alpha arrays	X: inserted helical bundle subdomain in T7 RNA polymerase (From Topology)	H: inserted helical bundle subdomain in T7 RNA polymerase (From Topology)	T: inserted helical bundle subdomain in T7 RNA polymerase	F: RNA_pol_1st	ECOD (1.6)
A [auth B]	KOG1038,RPOL_N	e8dh4B4	A: alpha bundles	X: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: fingers domain in bacteriophage RB69-like DNA polymerase I	F: KOG1038,RPOL_N	ECOD (1.6)
A [auth B]	RNA_pol_3rd	e8dh4B3	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: RNA_pol_3rd	ECOD (1.6)
E	RPOL_N_1	e8dh4E1	A: alpha arrays	X: HTH	H: HTH	T: HTH in T7 RNA polymerase	F: RPOL_N_1	ECOD (1.6)
E	RNA_pol_2nd	e8dh4E2	A: alpha arrays	X: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	H: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	T: helical bundle in Bacillus stearothermophilus-like DNA polymerase I	F: RNA_pol_2nd	ECOD (1.6)
E	RNA_pol_1st	e8dh4E4	A: alpha arrays	X: inserted helical bundle subdomain in T7 RNA polymerase (From Topology)	H: inserted helical bundle subdomain in T7 RNA polymerase (From Topology)	T: inserted helical bundle subdomain in T7 RNA polymerase	F: RNA_pol_1st	ECOD (1.6)
E	KOG1038,RPOL_N	e8dh4E5	A: alpha bundles	X: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: fingers domain in bacteriophage RB69-like DNA polymerase I	F: KOG1038,RPOL_N	ECOD (1.6)
E	RNA_pol_3rd	e8dh4E3	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: RNA_pol_3rd	ECOD (1.6)
I	RPOL_N_1	e8dh4I3	A: alpha arrays	X: HTH	H: HTH	T: HTH in T7 RNA polymerase	F: RPOL_N_1	ECOD (1.6)
I	RNA_pol_2nd	e8dh4I2	A: alpha arrays	X: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	H: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	T: helical bundle in Bacillus stearothermophilus-like DNA polymerase I	F: RNA_pol_2nd	ECOD (1.6)
I	RNA_pol_1st	e8dh4I5	A: alpha arrays	X: inserted helical bundle subdomain in T7 RNA polymerase (From Topology)	H: inserted helical bundle subdomain in T7 RNA polymerase (From Topology)	T: inserted helical bundle subdomain in T7 RNA polymerase	F: RNA_pol_1st	ECOD (1.6)
I	KOG1038,RPOL_N	e8dh4I4	A: alpha bundles	X: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: fingers domain in bacteriophage RB69-like DNA polymerase I	F: KOG1038,RPOL_N	ECOD (1.6)
I	RNA_pol_3rd	e8dh4I1	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: RNA_pol_3rd	ECOD (1.6)
M	RPOL_N_1	e8dh4M1	A: alpha arrays	X: HTH	H: HTH	T: HTH in T7 RNA polymerase	F: RPOL_N_1	ECOD (1.6)
M	RNA_pol_2nd	e8dh4M2	A: alpha arrays	X: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	H: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	T: helical bundle in Bacillus stearothermophilus-like DNA polymerase I	F: RNA_pol_2nd	ECOD (1.6)
M	RNA_pol_1st	e8dh4M5	A: alpha arrays	X: inserted helical bundle subdomain in T7 RNA polymerase (From Topology)	H: inserted helical bundle subdomain in T7 RNA polymerase (From Topology)	T: inserted helical bundle subdomain in T7 RNA polymerase	F: RNA_pol_1st	ECOD (1.6)
M	KOG1038,RPOL_N	e8dh4M4	A: alpha bundles	X: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: fingers domain in bacteriophage RB69-like DNA polymerase I	F: KOG1038,RPOL_N	ECOD (1.6)
M	RNA_pol_3rd	e8dh4M3	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: RNA_pol_3rd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], E, I, M	PF14700	DNA-directed RNA polymerase N-terminal (RPOL_N)	DNA-directed RNA polymerase N-terminal	This is the N-terminal domain of DNA-directed RNA polymerase. This domain has a role in interaction with regions of upstream promoter DNA and the nascent RNA chain, leading to the processivity of the enzyme [1]. In order to make mRNA transcripts the ...	This is the N-terminal domain of DNA-directed RNA polymerase. This domain has a role in interaction with regions of upstream promoter DNA and the nascent RNA chain, leading to the processivity of the enzyme [1]. In order to make mRNA transcripts the RNA polymerase undergoes a transition from the initiation phase (which only makes short fragments of RNA) to an elongation phase. This domain undergoes a structural change in the transition from initiation to elongation phase. The structural change results in abolition of the promoter binding site, creation of a channel accommodating the heteroduplex in the active site and formation of an exit tunnel which the RNA transcript passes through after peeling off the heteroduplex [2].	Domain
A [auth B], E, I, M	PF00940	DNA-dependent RNA polymerase (RNA_pol)	DNA-dependent RNA polymerase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth A], F, J, N	Template strand DNA	-	-	-
A [auth B], E, I, M	T7 RNA polymerase	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding mitochondrial promoter sequence-specific DNA 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 sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding mitochondrial promoter sequence-specific DNA 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	viral gene expression DNA-templated viral transcription viral process viral 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 viral gene expression DNA-templated viral transcription viral process viral 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	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, G, K, O	RNA	-	-	-
D, H, L, P	Non-template strand DNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], E, I, M	IPR029262	DNA-directed RNA polymerase, N-terminal	Domain
A [auth B], E, I, M	IPR002092	DNA-directed RNA polymerase, phage-type	Family
A [auth B], E, I, M	IPR024075	DNA-directed RNA polymerase, helix hairpin domain superfamily	Homologous Superfamily
A [auth B], E, I, M	IPR046950	DNA-directed RNA polymerase, C-terminal domain, phage-type	Domain
A [auth B], E, I, M	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A [auth B], E, I, M	IPR037159	DNA-directed RNA polymerase, N-terminal domain superfamily	Homologous Superfamily