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)
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)
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)
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)
N [auth B]	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)
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)
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)
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)
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)
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)
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)
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'	-	-	-
B [auth F], E [auth I], H [auth L], K [auth O]	5'-R(APAPCPUGPCPGPGPCPGPAPU)-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 nucleic acid binding	viral gene expression DNA-templated viral transcription viral process viral transcription	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

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]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
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]	IPR037159	DNA-directed RNA polymerase, N-terminal domain superfamily	Homologous Superfamily