Annotations: 4LK0

Crystal Structure Analysis of the E.coli holoenzyme/T7 Gp2 complex

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)
L	SCOP2B Superfamily	Sigma2 domain of RNA polymerase sigma factors	8038503	3001393	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sigma2 domain of RNA polymerase sigma factors	8038503	3001393	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	T7 Gp2 RNA polymerase inhibitor	8101177	3002717	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	T7 Gp2 RNA polymerase inhibitor	8101177	3002717	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)
H	Cupin_7	e4lk0H3	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Cupin_7	ECOD (v294.1)
G	Cupin_7	e4lk0G3	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Cupin_7	ECOD (v294.1)
B	Cupin_7	e4lk0B3	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Cupin_7	ECOD (v294.1)
A	Cupin_7	e4lk0A3	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Cupin_7	ECOD (v294.1)
I	His_biosynth	e4lk0I8	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: His_biosynth	ECOD (v294.1)
I	Chorismate_bind	e4lk0I19	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Chorismate_bind	ECOD (v294.1)
I	Pectate_lyase_2	e4lk0I9	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Pectate_lyase_2	ECOD (v294.1)
C	His_biosynth	e4lk0C8	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: His_biosynth	ECOD (v294.1)
C	Chorismate_bind	e4lk0C19	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Chorismate_bind	ECOD (v294.1)
C	Pectate_lyase_2	e4lk0C9	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Pectate_lyase_2	ECOD (v294.1)
J		e4lk0J2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
J	Peptidase_S26	e4lk0J9	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
D		e4lk0D1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
D	SH3_2	e4lk0D9	A: a/b three-layered sandwiches	X: SH3	H: SH3	T: SH3	F: SH3_2	ECOD (v294.1)
K	His_biosynth	e4lk0K1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: His_biosynth	ECOD (v294.1)
E	His_biosynth	e4lk0E1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: His_biosynth	ECOD (v294.1)
L	His_biosynth	e4lk0L1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: His_biosynth	ECOD (v294.1)
F	His_biosynth	e4lk0F1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: His_biosynth	ECOD (v294.1)
N	His_biosynth	e4lk0N1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: His_biosynth	ECOD (v294.1)
M	His_biosynth	e4lk0M1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: His_biosynth	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
H	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (4.3.0)
G	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
G	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)
I	2.40.270.10	Mainly Beta	Beta Barrel	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
I	3.90.1110.10	Alpha Beta	Alpha-Beta Complex	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
I	2.30.150.10	Mainly Beta	Roll	Rna Polymerase Beta Subunit	Chain: C, domain 4	CATH (4.3.0)
I	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	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
I	6.10.140.1670	Special	Helix non-globular	Helix Hairpins		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	2.40.270.10	Mainly Beta	Beta Barrel	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	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)
C	6.10.140.1670	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
J	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 (utative)
K	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)
L	1.10.601.10	Mainly Alpha	Orthogonal Bundle	RNA Polymerase Primary Sigma Factor	RNA Polymerase Primary Sigma Factor	CATH (4.3.0)
L	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	1.10.601.10	Mainly Alpha	Orthogonal Bundle	RNA Polymerase Primary Sigma Factor	RNA Polymerase Primary Sigma Factor	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)
N	3.10.20.510	Alpha Beta	Roll	Ubiquitin-like (UB roll)	RNA polymerase inhibitor	CATH (4.3.0)
M	3.10.20.510	Alpha Beta	Roll	Ubiquitin-like (UB roll)	RNA polymerase inhibitor	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
F, L	PF04539	Sigma-70 region 3 (Sigma70_r3)	Sigma-70 region 3	-	Family
F, L	PF00140	Sigma-70 factor, region 1.2 (Sigma70_r1_2)	Sigma-70 factor, region 1.2	-	Family
F, L	PF04542	Sigma-70 region 2 (Sigma70_r2)	Sigma-70 region 2	Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA ...	Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [1,2]. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation [1,2].	Domain
F, L	PF04545	Sigma-70, region 4 (Sigma70_r4)	Sigma-70, region 4	Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix fami ...	Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.	Domain
F, L	PF04546	Sigma-70, non-essential region (Sigma70_ner)	Sigma-70, non-essential region	The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function.	Domain
M, N	PF16857	RNA polymerase inhibitor (RNA_pol_inhib)	RNA polymerase inhibitor	This bacteriophage protein inhibits the bacterial host RNA polymerase by interacting with the RpoC subunit and inhibiting the formation of a promoter complex [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, G, H	DNA-directed RNA polymerase subunit alpha	-	-	-
C, I	DNA-directed RNA polymerase subunit beta	-	-	-
D, J	DNA-directed RNA polymerase subunit beta'	-	-	-
E, K	DNA-directed RNA polymerase subunit omega	-	-	-
F, L	RNA polymerase sigma factor RpoD	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region 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 DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region 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 transcription regulator activity DNA-binding transcription factor activity sigma factor activity	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of DNA-templated transcription initiation DNA-templated transcription initiation response to stimulus response to stress response to heat response to abiotic stimulus response to temperature stimulus	protein-containing complex intracellular anatomical structure catalytic complex transferase complex transferase complex, transferring phosphorus-containing groups cellular anatomical structure cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex sigma factor antagonist complex transcription regulator complex
M, N	Bacterial RNA polymerase inhibitor	-	symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host transcription symbiont-mediated perturbation of host transcription	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F, L	IPR007627	RNA polymerase sigma-70 region 2	Domain
F, L	IPR000943	RNA polymerase sigma-70	Domain
F, L	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
F, L	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
F, L	IPR007630	RNA polymerase sigma-70 region 4	Domain
F, L	IPR014284	RNA polymerase sigma-70-like domain	Domain
F, L	IPR007624	RNA polymerase sigma-70 region 3	Domain
F, L	IPR028630	RNA polymerase sigma factor RpoD	Family
F, L	IPR050239	Sigma-70 factor family, RNA polymerase initiation factors	Family
F, L	IPR007127	RNA polymerase sigma factor 70, region 1.1	Domain
F, L	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
F, L	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
F, L	IPR012760	RNA polymerase sigma factor RpoD, C-terminal	Domain
F, L	IPR007631	RNA polymerase sigma factor 70, non-essential domain	Domain
F, L	IPR042189	Sigma-70 factor, region 1.1 superfamily	Homologous Superfamily
M, N	IPR016412	RNA polymerase inhibitor	Family
M, N	IPR038715	RNA polymerase inhibitor superfamily	Homologous Superfamily