4QIW | pdb_00004qiw

Crystal structure of euryarchaeal RNA polymerase from Thermococcus kodakarensis

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
T [auth U]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8080738	3001655	SCOP2B (2022-06-29)
I [auth L]	SCOP2 Family	RBP11/RpoL	8080737	4003562	SCOP2 (2022-06-29)
I [auth L]	SCOP2 Superfamily	RBP11-like subunits of RNA polymerase	8080738	3001655	SCOP2 (2022-06-29)
S [auth T]	SCOP2B Superfamily	RPB6/omega subunit-like	8078383	3000189	SCOP2B (2022-06-29)
H [auth K]	SCOP2 Family	RPB6	8078382	4001505	SCOP2 (2022-06-29)
H [auth K]	SCOP2 Superfamily	RPB6/omega subunit-like	8078383	3000189	SCOP2 (2022-06-29)
R [auth S]	SCOP2B Superfamily	RPB5-like RNA polymerase subunit	8063568	3001722	SCOP2B (2022-06-29)
G [auth H]	SCOP2 Family	RPB5	8063567	4001502	SCOP2 (2022-06-29)
G [auth H]	SCOP2 Superfamily	RPB5-like RNA polymerase subunit	8063568	3001722	SCOP2 (2022-06-29)
Q [auth R]	SCOP2B Superfamily	HRDC-like	8086299	3000132	SCOP2B (2022-06-29)
F	SCOP2 Family	RNA polymerase II subunit RBP4 (RpoF)	8086298	4002844	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	HRDC-like	8086299	3000132	SCOP2 (2022-06-29)
U [auth V]	SCOP2B Superfamily	RNA polymerase subunit RPB10	8063360	3001213	SCOP2B (2022-06-29)
J [auth N]	SCOP2 Family	RNA polymerase subunit RPB10	8063359	4000742	SCOP2 (2022-06-29)
J [auth N]	SCOP2 Superfamily	RNA polymerase subunit RPB10	8063360	3001213	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
T [auth U]	Stap_Strp_tox_C	e4qiwU1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: Stap_Strp_tox_C	ECOD (v294.1)
I [auth L]	Stap_Strp_tox_C	e4qiwL1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: Stap_Strp_tox_C	ECOD (v294.1)
S [auth T]	ERG4_ERG24	e4qiwT1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: N-terminal domain of Delta(14)-sterol reductase, MaSR1	F: ERG4_ERG24	ECOD (v294.1)
H [auth K]	RNA_pol_Rpb6	e4qiwK1	A: a/b three-layered sandwiches	X: Insertion subdomain in DsbA-like	H: hypothetical protein RUMGNA_01148-related	T: hypothetical protein RUMGNA_01148-related	F: RNA_pol_Rpb6	ECOD (v294.1)
R [auth S]	Stap_Strp_tox_C	e4qiwS1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: Stap_Strp_tox_C	ECOD (v294.1)
G [auth H]	Stap_Strp_tox_C	e4qiwH1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: Stap_Strp_tox_C	ECOD (v294.1)
Q [auth R]	Stap_Strp_tox_C	e4qiwR1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: Stap_Strp_tox_C	ECOD (v294.1)
F	Stap_Strp_tox_C	e4qiwF1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: Stap_Strp_tox_C	ECOD (v294.1)
P [auth Q]	Stap_Strp_tox_C	e4qiwQ1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: Stap_Strp_tox_C	ECOD (v294.1)
E	Stap_Strp_tox_C	e4qiwE1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: Stap_Strp_tox_C	ECOD (v294.1)
O		e4qiwO1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F:	ECOD (v294.1)
D		e4qiwD1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F:	ECOD (v294.1)
N [auth M]	EPSP_synthase	e4qiwM1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (v294.1)
C	EPSP_synthase	e4qiwC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (v294.1)
M [auth J]	ACR_tran	e4qiwJ1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: ACR_tran	ECOD (v294.1)
M [auth J]	RNA_pol_Rpb2_6	e4qiwJ7	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: RNA_pol_Rpb2_6	ECOD (v294.1)
M [auth J]		e4qiwJ3	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F:	ECOD (v294.1)
B	Stap_Strp_tox_C	e4qiwB6	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: Stap_Strp_tox_C	ECOD (v294.1)
B	RNA_pol_Rpb2_6	e4qiwB7	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: RNA_pol_Rpb2_6	ECOD (v294.1)
B	VipB_2	e4qiwB3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: VipB_2	ECOD (v294.1)
B		e4qiwB2	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F:	ECOD (v294.1)
V [auth W]	ACR_tran	e4qiwW1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: ACR_tran	ECOD (v294.1)
K [auth P]	Stap_Strp_tox_C	e4qiwP1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: Stap_Strp_tox_C	ECOD (v294.1)
U [auth V]	Stap_Strp_tox_C	e4qiwV1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: Stap_Strp_tox_C	ECOD (v294.1)
J [auth N]	Stap_Strp_tox_C	e4qiwN1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: Stap_Strp_tox_C	ECOD (v294.1)
L [auth I]		e4qiwI1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F:	ECOD (v294.1)
A		e4qiwA1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
T [auth U]	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
I [auth L]	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
S [auth T]	3.90.940.10	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit	RNA polymerase subunit, RPB6/omega	CATH (4.3.0)
H [auth K]	3.90.940.10	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit	RNA polymerase subunit, RPB6/omega	CATH (4.3.0)
R [auth S]	3.90.940.20	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit	RPB5-like RNA polymerase subunit	CATH (4.3.0)
G [auth H]	3.90.940.20	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit	RPB5-like RNA polymerase subunit	CATH (4.3.0)
Q [auth R]	6.10.140.10	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
Q [auth R]	1.10.150.80	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
F	6.10.140.10	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
F	1.10.150.80	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
P [auth Q]	3.30.1490.120	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
P [auth Q]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
E	3.30.1490.120	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
E	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
O	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
O	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (4.3.0)
O	3.30.70.3110	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
D	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
D	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (4.3.0)
D	3.30.70.3110	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
N [auth M]	1.10.150.390	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
C	1.10.150.390	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
M [auth J]	3.90.1110.10	Alpha Beta	Alpha-Beta Complex	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
M [auth J]	3.90.1070.20	Alpha Beta	Alpha-Beta Complex	Hypothetical Protein Ta0175	Chain: A, domain 2	CATH (4.3.0)
M [auth J]	2.40.270.10	Mainly Beta	Beta Barrel	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
M [auth J]	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
M [auth J]	3.90.1800.10	Alpha Beta	Alpha-Beta Complex	DCoH-like	RNA polymerase alpha subunit dimerisation domain	CATH (4.3.0)
B	3.90.1110.10	Alpha Beta	Alpha-Beta Complex	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
B	3.90.1070.20	Alpha Beta	Alpha-Beta Complex	Hypothetical Protein Ta0175	Chain: A, domain 2	CATH (4.3.0)
B	2.40.270.10	Mainly Beta	Beta Barrel	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
B	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
B	3.90.1800.10	Alpha Beta	Alpha-Beta Complex	DCoH-like	RNA polymerase alpha subunit dimerisation domain	CATH (4.3.0)
V [auth W]	2.20.28.30	Mainly Beta	Single Sheet	Rubrerythrin, domain 2	RNA polymerase ii, chain L	CATH (4.3.0)
K [auth P]	2.20.28.30	Mainly Beta	Single Sheet	Rubrerythrin, domain 2	RNA polymerase ii, chain L	CATH (4.3.0)
U [auth V]	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
J [auth N]	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
L [auth I]	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
L [auth I]	3.30.1490.180	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
L [auth I]	1.10.274.100	Mainly Alpha	Orthogonal Bundle	Enzyme I	Chain A, domain 2	CATH (4.3.0)
L [auth I]	1.10.132.30	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.3.0)
A	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
A	3.30.1490.180	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
A	1.10.274.100	Mainly Alpha	Orthogonal Bundle	Enzyme I	Chain A, domain 2	CATH (4.3.0)
A	1.10.132.30	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth L], T [auth U]	PF13656	RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L_2)	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. Many of the members of this family carry only the N-terminal region of Rpb11.	Domain
H [auth K], S [auth T]	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family
G [auth H], R [auth S]	PF01191	RNA polymerase Rpb5, C-terminal domain (RNA_pol_Rpb5_C)	RNA polymerase Rpb5, C-terminal domain	The assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain.	Domain
F, Q [auth R]	PF03874	RNA polymerase Rpb4 (RNA_pol_Rpb4)	RNA polymerase Rpb4	-	Family
E, P [auth Q]	PF03876	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 (SHS2_Rpb7-N)	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397	Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at leas ...	Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA [2]. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction [3].	Domain
E, P [auth Q]	PF00575	S1 RNA binding domain (S1)	S1 RNA binding domain	The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.	Domain
D, O	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
D, O	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
B, M [auth J]	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
B, M [auth J]	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
B, M [auth J]	PF04566	RNA polymerase Rpb2, domain 4 (RNA_pol_Rpb2_4)	RNA polymerase Rpb2, 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). Domain 4, is also known as the external 2 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). Domain 4, is also known as the external 2 domain [1].	Domain
B, M [auth J]	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
B, M [auth J]	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
B, M [auth J]	PF04567	RNA polymerase Rpb2, domain 5 (RNA_pol_Rpb2_5)	RNA polymerase Rpb2, 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). Domain 5, is also known as the external 2 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). Domain 5, is also known as the external 2 domain [1].	Domain
J [auth N], U [auth V]	PF01194	RNA polymerases N / 8 kDa subunit (RNA_pol_N)	RNA polymerases N / 8 kDa subunit		Domain
A, L [auth I]	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
A, L [auth I]	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
A, L [auth I]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth L], T [auth U]	DNA-directed RNA polymerase subunit L	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
H [auth K], S [auth T]	DNA-directed RNA polymerase subunit K	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	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome 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
G [auth H], R [auth S]	DNA-directed RNA polymerase subunit H	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	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
F, Q [auth R]	DNA-directed RNA polymerase, subunit F	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule 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 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 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, P [auth Q]	DNA-directed RNA polymerase, subunit E'	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 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 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, O	DNA-directed RNA polymerase subunit D	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 protein binding protein dimerization activity	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, N [auth M]	DNA-directed RNA polymerase subunit A''	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	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome 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
B, M [auth J]	DNA-directed RNA polymerase	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 cation binding transition metal ion binding zinc ion binding ion binding metal 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	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
K [auth P], V [auth W]	DNA-directed RNA polymerase subunit P	DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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 DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome 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
J [auth N], U [auth V]	DNA-directed RNA polymerase subunit N	DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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 DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome 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
A, L [auth I]	DNA-directed RNA polymerase	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	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
I [auth L], T [auth U]	IPR022905	DNA-directed RNA polymerase subunit Rpo11-like	Family
I [auth L], T [auth U]	IPR009025	DNA-directed RNA polymerase, RBP11-like dimerisation domain	Domain
I [auth L], T [auth U]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
I [auth L], T [auth U]	IPR008193	DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site	Conserved Site
H [auth K], S [auth T]	IPR020708	DNA-directed RNA polymerase, 14-18kDa subunit, conserved site	Conserved Site
H [auth K], S [auth T]	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
H [auth K], S [auth T]	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
H [auth K], S [auth T]	IPR006111	Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit	Family
G [auth H], R [auth S]	IPR014381	DNA-directed RNA polymerase subunit Rpo5/Rpb5	Family
G [auth H], R [auth S]	IPR035913	RPB5-like RNA polymerase subunit superfamily	Homologous Superfamily
G [auth H], R [auth S]	IPR000783	RNA polymerase, subunit H/Rpb5 C-terminal	Domain
G [auth H], R [auth S]	IPR020608	RNA polymerase, subunit H/Rpb5, conserved site	Conserved Site
F, Q [auth R]	IPR005574	RNA polymerase subunit Rpb4/RPC9	Family
F, Q [auth R]	IPR044876	HRDC domain superfamily	Homologous Superfamily
F, Q [auth R]	IPR010997	HRDC-like superfamily	Homologous Superfamily
F, Q [auth R]	IPR010924	DNA-directed RNA polymerase subunit Rpo4	Family
E, P [auth Q]	IPR046399	DNA-directed RNA polymerase subunit Rpo7	Family
E, P [auth Q]	IPR036898	RNA polymerase Rpb7-like, N-terminal domain superfamily	Homologous Superfamily
E, P [auth Q]	IPR004519	DNA-directed RNA polymerase, subunit E/RPC8	Family
E, P [auth Q]	IPR003029	S1 domain	Domain
E, P [auth Q]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
E, P [auth Q]	IPR045113	RNA polymerase subunit Rpb7-like	Family
E, P [auth Q]	IPR005576	RNA polymerase Rpb7-like , N-terminal	Domain
D, O	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
D, O	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
D, O	IPR050518	Archaeal Rpo3/Eukaryotic RPB3 RNA Polymerase Subunit	Family
D, O	IPR022842	DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1	Family
D, O	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
D, O	IPR001514	DNA-directed RNA polymerase, 30-40kDa subunit, conserved site	Conserved Site
D, O	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
C, N [auth M]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
C, N [auth M]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
C, N [auth M]	IPR012757	DNA-directed RNA polymerase subunit Rpo1C	Family
B, M [auth J]	IPR007642	RNA polymerase Rpb2, domain 2	Domain
B, M [auth J]	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
B, M [auth J]	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
B, M [auth J]	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
B, M [auth J]	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
B, M [auth J]	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
B, M [auth J]	IPR007645	RNA polymerase Rpb2, domain 3	Domain
B, M [auth J]	IPR007646	RNA polymerase Rpb2, domain 4	Domain
B, M [auth J]	IPR007647	RNA polymerase Rpb2, domain 5	Domain
B, M [auth J]	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
B, M [auth J]	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
B, M [auth J]	IPR007641	RNA polymerase Rpb2, domain 7	Domain
B, M [auth J]	IPR019969	DNA-directed RNA polymerase subunit Rpo2	Family
K [auth P], V [auth W]	IPR006591	RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4	Family
K [auth P], V [auth W]	IPR023464	DNA-directed RNA polymerase subunit Rpo12	Family
K [auth P], V [auth W]	IPR029040	RNA polymerase subunit RPABC4/transcription elongation factor Spt4	Homologous Superfamily
J [auth N], U [auth V]	IPR023580	RNA polymerase subunit RPB10	Homologous Superfamily
J [auth N], U [auth V]	IPR020789	RNA polymerases, subunit N, zinc binding site	Binding Site
J [auth N], U [auth V]	IPR000268	DNA-directed RNA polymerase subunit RPABC5/Rpb10	Family
A, L [auth I]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
A, L [auth I]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
A, L [auth I]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
A, L [auth I]	IPR012758	DNA-directed RNA polymerase subunit Rpo1N	Family
A, L [auth I]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
A, L [auth I]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
A, L [auth I]	IPR000722	RNA polymerase, alpha subunit	Domain
A, L [auth I]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
A, L [auth I]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
A, L [auth I]	IPR006592	RNA polymerase, N-terminal	Domain
A, L [auth I]	IPR007080	RNA polymerase Rpb1, domain 1	Domain