1S0V

Structural basis for substrate selection by T7 RNA polymerase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
M [auth A]	d1s0va_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	T7 RNA polymerase	T7 RNA polymerase	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
O [auth C]	d1s0vc_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	T7 RNA polymerase	T7 RNA polymerase	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
N [auth B]	d1s0vb_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	T7 RNA polymerase	T7 RNA polymerase	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
P [auth D]	d1s0vd_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	T7 RNA polymerase	T7 RNA polymerase	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
M [auth A]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
M [auth A]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
O [auth C]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
O [auth C]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
N [auth B]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
N [auth B]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
P [auth D]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
P [auth D]	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)
M [auth A]	RPOL_N_1	e1s0vA6	A: alpha arrays	X: HTH	H: HTH	T: HTH in T7 RNA polymerase	F: RPOL_N_1	ECOD (1.6)
M [auth A]	RNA_pol_2nd	e1s0vA1	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 [auth A]	RNA_pol_1st	e1s0vA3	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 [auth A]	KOG1038,RPOL_N	e1s0vA2	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 [auth A]	RNA_pol_3rd	e1s0vA5	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)
O [auth C]	RPOL_N_1	e1s0vC4	A: alpha arrays	X: HTH	H: HTH	T: HTH in T7 RNA polymerase	F: RPOL_N_1	ECOD (1.6)
O [auth C]	RNA_pol_2nd	e1s0vC1	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)
O [auth C]	RNA_pol_1st	e1s0vC3	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)
O [auth C]	KOG1038,RPOL_N	e1s0vC2	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)
O [auth C]	RNA_pol_3rd	e1s0vC5	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)
N [auth B]	RPOL_N_1	e1s0vB2	A: alpha arrays	X: HTH	H: HTH	T: HTH in T7 RNA polymerase	F: RPOL_N_1	ECOD (1.6)
N [auth B]	RNA_pol_2nd	e1s0vB1	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)
N [auth B]	RNA_pol_1st	e1s0vB3	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)
N [auth B]	KOG1038,RPOL_N	e1s0vB4	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)
N [auth B]	RNA_pol_3rd	e1s0vB5	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)
P [auth D]	RPOL_N_1	e1s0vD6	A: alpha arrays	X: HTH	H: HTH	T: HTH in T7 RNA polymerase	F: RPOL_N_1	ECOD (1.6)
P [auth D]	RNA_pol_2nd	e1s0vD1	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)
P [auth D]	RNA_pol_1st	e1s0vD3	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)
P [auth D]	KOG1038,RPOL_N	e1s0vD4	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)
P [auth D]	RNA_pol_3rd	e1s0vD5	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
M [auth A]	1.10.1320.10	Mainly Alpha	Orthogonal Bundle	T7 RNA polymerase	domain 1	CATH (4.3.0)
M [auth A]	1.10.287.260	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
M [auth A]	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
M [auth A]	1.10.287.280	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
M [auth A]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
O [auth C]	1.10.1320.10	Mainly Alpha	Orthogonal Bundle	T7 RNA polymerase	domain 1	CATH (4.3.0)
O [auth C]	1.10.287.260	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
O [auth C]	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
O [auth C]	1.10.287.280	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
O [auth C]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
N [auth B]	1.10.1320.10	Mainly Alpha	Orthogonal Bundle	T7 RNA polymerase	domain 1	CATH (4.3.0)
N [auth B]	1.10.287.260	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
N [auth B]	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
N [auth B]	1.10.287.280	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
N [auth B]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
P [auth D]	1.10.1320.10	Mainly Alpha	Orthogonal Bundle	T7 RNA polymerase	domain 1	CATH (4.3.0)
P [auth D]	1.10.287.260	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
P [auth D]	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
P [auth D]	1.10.287.280	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
P [auth D]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
M [auth A], N [auth B], O [auth C], P [auth D]	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
M [auth A], N [auth B], O [auth C], P [auth D]	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
A [auth E], D [auth H], G [auth K], J [auth N]	5'-D(GGPGPAPAPTPCPGPAPTPAPTPCPGPCPCPGPC)-3'	-	-	-
C [auth G], F [auth J], I [auth M], L [auth P]	5'-D(GPTPCPGPAPTPTPCPCPC)-3'	-	-	-
M [auth A], N [auth B], O [auth C], P [auth D]	DNA-directed RNA polymerase	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	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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance 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
B [auth F], E [auth I], H [auth L], K [auth O]	5'-R(APAPCPUGPCPGPGPCPGPAPU)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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