1SMY | pdb_00001smy

Structural basis for transcription regulation by alarmone ppGpp

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)
L [auth P]	d1smyp1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	Sigma3 domain	Sigma70	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
L [auth P]	d1smyp2	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	Sigma4 domain	Sigma70 (SigA, RpoD)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
L [auth P]	d1smyp3	All alpha proteins	Sigma2 domain of RNA polymerase sigma factors	Sigma2 domain of RNA polymerase sigma factors	Sigma2 domain of RNA polymerase sigma factors	Sigma70	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
F	d1smyf1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	Sigma3 domain	Sigma70	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
F	d1smyf2	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	Sigma4 domain	Sigma70 (SigA, RpoD)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
F	d1smyf3	All alpha proteins	Sigma2 domain of RNA polymerase sigma factors	Sigma2 domain of RNA polymerase sigma factors	Sigma2 domain of RNA polymerase sigma factors	Sigma70	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
K [auth O]	d1smyo_	All alpha proteins	RPB6/omega subunit-like	RPB6/omega subunit-like	RNA polymerase omega subunit	RNA polymerase omega subunit	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
E	d1smye_	All alpha proteins	RPB6/omega subunit-like	RPB6/omega subunit-like	RNA polymerase omega subunit	RNA polymerase omega subunit	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
J [auth N]	d1smyn_	Multi-domain proteins (alpha and beta)	beta and beta-prime subunits of DNA dependent RNA-polymerase	beta and beta-prime subunits of DNA dependent RNA-polymerase	RNA-polymerase beta-prime	RNA-polymerase beta-prime	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
D	d1smyd_	Multi-domain proteins (alpha and beta)	beta and beta-prime subunits of DNA dependent RNA-polymerase	beta and beta-prime subunits of DNA dependent RNA-polymerase	RNA-polymerase beta-prime	RNA-polymerase beta-prime	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
I [auth M]	d1smym_	Multi-domain proteins (alpha and beta)	beta and beta-prime subunits of DNA dependent RNA-polymerase	beta and beta-prime subunits of DNA dependent RNA-polymerase	RNA-polymerase beta	RNA-polymerase beta	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
C	d1smyc_	Multi-domain proteins (alpha and beta)	beta and beta-prime subunits of DNA dependent RNA-polymerase	beta and beta-prime subunits of DNA dependent RNA-polymerase	RNA-polymerase beta	RNA-polymerase beta	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
H [auth L]	d1smyl1	Alpha and beta proteins (a+b)	DCoH-like	RBP11-like subunits of RNA polymerase	RNA polymerase alpha subunit dimerisation domain	RNA polymerase alpha	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
H [auth L]	d1smyl2	Alpha and beta proteins (a+b)	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	RNA polymerase alpha subunit	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
G [auth K]	d1smyk1	Alpha and beta proteins (a+b)	DCoH-like	RBP11-like subunits of RNA polymerase	RNA polymerase alpha subunit dimerisation domain	RNA polymerase alpha	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
G [auth K]	d1smyk2	Alpha and beta proteins (a+b)	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	RNA polymerase alpha subunit	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d1smyb1	Alpha and beta proteins (a+b)	DCoH-like	RBP11-like subunits of RNA polymerase	RNA polymerase alpha subunit dimerisation domain	RNA polymerase alpha	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d1smyb2	Alpha and beta proteins (a+b)	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	RNA polymerase alpha subunit	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d1smya1	Alpha and beta proteins (a+b)	DCoH-like	RBP11-like subunits of RNA polymerase	RNA polymerase alpha subunit dimerisation domain	RNA polymerase alpha	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d1smya2	Alpha and beta proteins (a+b)	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	RNA polymerase alpha subunit	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2 Family	Sigma3 domain	8027235	4003497	SCOP2 (2022-06-29)
F	SCOP2 Family	Sigma4 domain	8027236	4003503	SCOP2 (2022-06-29)
F	SCOP2 Family	Sigma2 domain of RNA polymerase sigma factors	8027237	4003741	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	Sigma factor domain-like	8039614	3000953	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	Sigma factor domain-like	8039615	3000953	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	Sigma2 domain of RNA polymerase sigma factors	8039616	3001393	SCOP2 (2022-06-29)
K [auth O]	SCOP2B Superfamily	RPB6/omega subunit-like	8039612	3000189	SCOP2B (2022-06-29)
E	SCOP2 Family	RNA polymerase omega subunit	8027233	4003034	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	RPB6/omega subunit-like	8039612	3000189	SCOP2 (2022-06-29)
J [auth N]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8039613	3001330	SCOP2B (2022-06-29)
D	SCOP2 Family	RNA-polymerase beta-prime subunit	8027234	4003714	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Two-barrel nucleic acid polymerases	8039613	3001330	SCOP2 (2022-06-29)
I [auth M]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8039611	3001330	SCOP2B (2022-06-29)
I [auth M]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8039611	3001330	SCOP2B (2022-06-29)
C	SCOP2 Family	RNA-polymerase beta subunit	8027232	4003708	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Two-barrel nucleic acid polymerases	8039611	3001330	SCOP2 (2022-06-29)
A	SCOP2 Family	RNA polymerase alpha subunit dimerisation domain	8027225	4001475	SCOP2 (2022-06-29)
A	SCOP2 Family	Insert subdomain of RNA polymerase alpha subunit	8027228	4002623	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RBP11-like subunits of RNA polymerase	8039604	3001655	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Insert subdomain of RNA polymerase alpha subunit	8039607	3001500	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L [auth P]	e1smyP1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Fe_dep_repress	F:	ECOD (20:10:01)
L [auth P]	e1smyP3	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Propep_M14	F:	ECOD (20:10:01)
F	e1smyF1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Fe_dep_repress	F:	ECOD (20:10:01)
F	e1smyF3	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Propep_M14	F:	ECOD (20:10:01)
K [auth O]	e1smyO1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: IMS_HHH	F:	ECOD (20:10:01)
E	e1smyE1	A: RPB6/omega subunit-like	X: RPB6/omega subunit-like	H: RNA polymerase omega subunit	T: RNA_pol_Rpb6	F:	ECOD (20:10:01)
J [auth N]	e1smyN1	A: CCHC-type 1 zinc finger	X: LEM/SAP HeH motif	H: LEM/SAP HeH motif	T: GP120	F:	ECOD (20:10:01)
D	e1smyD1	A: CCHC-type 1 zinc finger	X: LEM/SAP HeH motif	H: LEM/SAP HeH motif	T: GP120	F:	ECOD (20:10:01)
I [auth M]	e1smyM4	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
I [auth M]	e1smyM6	A: UBC-like	X: UBC-like	H: Concanavalin A-like lectins/glucanases	T: Pyr_redox_2	F:	ECOD (20:10:01)
I [auth M]	e1smyM8	A: Four-helical up-and-down bundle	X: Thymidylate synthase/dCMP hydroxymethylase	H: Thymidylate synthase/dCMP hydroxymethylase	T: Pectate_lyase_2	F:	ECOD (20:10:01)
C	e1smyC4	A: N-terminal domain in beta subunit of DNA dependent RNA-polymerase	X: N-terminal domain in beta subunit of DNA dependent RNA-polymerase	H: N-terminal domain in beta subunit of DNA dependent RNA-polymerase	T: RNA_pol_Rpb2_1,RNA_pol_Rpb2_3	F:	ECOD (20:10:01)
C	e1smyC5	A: insertion domain in beta subunit of DNA dependent RNA-polymerase	X: insertion domain in beta subunit of DNA dependent RNA-polymerase	H: insertion domain in beta subunit of DNA dependent RNA-polymerase	T: RNA_pol_Rpb2_2	F:	ECOD (20:10:01)
C	e1smyC7	A: C-terminal domain in beta subunit of DNA dependent RNA-polymerase	X: C-terminal domain in beta subunit of DNA dependent RNA-polymerase	H: C-terminal domain in beta subunit of DNA dependent RNA-polymerase	T: RNA_pol_Rpb2_6,RNA_pol_Rpb2_7	F:	ECOD (20:10:01)
C	e1smyC2	A: L-aspartase N-terminal domain-like	X: L-aspartase N-terminal domain-like	H: L-aspartase N-terminal domain-like	T:	F:	ECOD (20:10:01)
C	e1smyC8	A: Glycosyl hydrolase domain-like	X: Glycoside hydrolase family 127 middle domain-related	H: Glycoside hydrolase family 127 middle domain-related	T: RNA_pol_Rpb2_6	F:	ECOD (20:10:01)
H [auth L]	e1smyL1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
H [auth L]	e1smyL2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
G [auth K]	e1smyK1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
G [auth K]	e1smyK2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
B	e1smyB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
B	e1smyB2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
A	e1smyA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
A	e1smyA2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L [auth P]	1.20.120.1810	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
L [auth P]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
F	1.20.120.1810	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
F	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
K [auth O]	3.90.940.10	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit	RNA polymerase subunit, RPB6/omega	CATH (4.3.0)
E	3.90.940.10	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit	RNA polymerase subunit, RPB6/omega	CATH (4.3.0)
J [auth N]	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
J [auth N]	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
J [auth N]	1.10.274.100	Mainly Alpha	Orthogonal Bundle	Enzyme I	Chain A, domain 2	CATH (4.3.0)
J [auth N]	1.10.132.30	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.3.0)
D	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
D	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
D	1.10.274.100	Mainly Alpha	Orthogonal Bundle	Enzyme I	Chain A, domain 2	CATH (4.3.0)
D	1.10.132.30	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.3.0)
I [auth M]	2.40.270.10	Mainly Beta	Beta Barrel	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
I [auth M]	3.90.1100.10	Alpha Beta	Alpha-Beta Complex	Rna Polymerase Beta Subunit	Chain: C,domain 2	CATH (4.3.0)
I [auth M]	3.90.1110.10	Alpha Beta	Alpha-Beta Complex	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
I [auth M]	2.30.150.10	Mainly Beta	Roll	Rna Polymerase Beta Subunit	Chain: C, domain 4	CATH (4.3.0)
I [auth M]	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
I [auth M]	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
C	2.40.270.10	Mainly Beta	Beta Barrel	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
C	3.90.1100.10	Alpha Beta	Alpha-Beta Complex	Rna Polymerase Beta Subunit	Chain: C,domain 2	CATH (4.3.0)
C	3.90.1110.10	Alpha Beta	Alpha-Beta Complex	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
C	2.30.150.10	Mainly Beta	Roll	Rna Polymerase Beta Subunit	Chain: C, domain 4	CATH (4.3.0)
C	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
C	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
H [auth L]	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
H [auth L]	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (4.3.0)
G [auth K]	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
G [auth K]	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (4.3.0)
B	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
B	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (4.3.0)
A	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
A	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, K [auth O]	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family
D, J [auth N]	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, J [auth N]	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, J [auth N]	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, J [auth N]	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, J [auth N]	PF21668	DNA-directed RNA polymerase subunit beta', hybrid domain (RPOC_hybrid)	DNA-directed RNA polymerase subunit beta', hybrid domain	This is a hybrid domain found in DNA-directed RNA polymerase subunit beta' (RPOC) found in Deinococcus [1-5].	Domain
D, J [auth N]	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 dom ...	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
C, I [auth M]	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, I [auth M]	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, I [auth M]	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, I [auth M]	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, I [auth M]	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
C, I [auth M]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F, L [auth P]	principal sigma factor	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity sigma factor activity	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation 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 RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation 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
E, K [auth O]	RNA POLYMERASE OMEGA SUBUNIT	DNA binding binding nucleic acid binding DNA-directed 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
D, J [auth N]	DNA-directed RNA polymerase beta' chain	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding DNA-directed 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 cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding DNA-directed 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
C, I [auth M]	DNA-directed RNA polymerase beta chain	DNA binding binding nucleic acid binding DNA-directed 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 DNA binding binding nucleic acid binding DNA-directed 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
A, B, G [auth K], H [auth L]	DNA-directed RNA polymerase alpha chain	DNA binding binding nucleic acid binding protein binding protein dimerization activity DNA-directed 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F, L [auth P]	IPR007627	RNA polymerase sigma-70 region 2	Domain
F, L [auth P]	IPR000943	RNA polymerase sigma-70	Domain
F, L [auth P]	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
F, L [auth P]	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
F, L [auth P]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
F, L [auth P]	IPR012760	RNA polymerase sigma factor RpoD, C-terminal	Domain
F, L [auth P]	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
F, L [auth P]	IPR007630	RNA polymerase sigma-70 region 4	Domain
F, L [auth P]	IPR014284	RNA polymerase sigma-70-like domain	Domain
F, L [auth P]	IPR007624	RNA polymerase sigma-70 region 3	Domain
F, L [auth P]	IPR028630	RNA polymerase sigma factor RpoD	Family
F, L [auth P]	IPR050239	Sigma-70 factor family, RNA polymerase initiation factors	Family
E, K [auth O]	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
E, K [auth O]	IPR003716	DNA-directed RNA polymerase, omega subunit	Family
E, K [auth O]	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
D, J [auth N]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
D, J [auth N]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
D, J [auth N]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
D, J [auth N]	IPR012754	DNA-directed RNA polymerase, subunit beta-prime, bacterial type	Family
D, J [auth N]	IPR048566	DNA-directed RNA polymerase subunit beta', hybrid domain	Domain
D, J [auth N]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
D, J [auth N]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
D, J [auth N]	IPR000722	RNA polymerase, alpha subunit	Domain
D, J [auth N]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
D, J [auth N]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
D, J [auth N]	IPR006592	RNA polymerase, N-terminal	Domain
D, J [auth N]	IPR007080	RNA polymerase Rpb1, domain 1	Domain
C, I [auth M]	IPR007642	RNA polymerase Rpb2, domain 2	Domain
C, I [auth M]	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
C, I [auth M]	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
C, I [auth M]	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
C, I [auth M]	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
C, I [auth M]	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
C, I [auth M]	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
C, I [auth M]	IPR007645	RNA polymerase Rpb2, domain 3	Domain
C, I [auth M]	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
C, I [auth M]	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
C, I [auth M]	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
C, I [auth M]	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
C, I [auth M]	IPR007641	RNA polymerase Rpb2, domain 7	Domain
A, B, G [auth K], H [auth L]	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
A, B, G [auth K], H [auth L]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
A, B, G [auth K], H [auth L]	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
A, B, G [auth K], H [auth L]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
A, B, G [auth K], H [auth L]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
A, B, G [auth K], H [auth L]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily