3K4G

Crystal structure of E. coli RNA polymerase alpha subunit C-terminal domain

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3k4gb_	All alpha proteins	SAM domain-like	C-terminal domain of RNA polymerase alpha subunit	C-terminal domain of RNA polymerase alpha subunit	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
F	d3k4gf_	All alpha proteins	SAM domain-like	C-terminal domain of RNA polymerase alpha subunit	C-terminal domain of RNA polymerase alpha subunit	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
H	d3k4gh_	All alpha proteins	SAM domain-like	C-terminal domain of RNA polymerase alpha subunit	C-terminal domain of RNA polymerase alpha subunit	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3k4ga_	All alpha proteins	SAM domain-like	C-terminal domain of RNA polymerase alpha subunit	C-terminal domain of RNA polymerase alpha subunit	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d3k4gc_	All alpha proteins	SAM domain-like	C-terminal domain of RNA polymerase alpha subunit	C-terminal domain of RNA polymerase alpha subunit	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d3k4gd_	All alpha proteins	SAM domain-like	C-terminal domain of RNA polymerase alpha subunit	C-terminal domain of RNA polymerase alpha subunit	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
E	d3k4ge_	All alpha proteins	SAM domain-like	C-terminal domain of RNA polymerase alpha subunit	C-terminal domain of RNA polymerase alpha subunit	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
G	d3k4gg_	All alpha proteins	SAM domain-like	C-terminal domain of RNA polymerase alpha subunit	C-terminal domain of RNA polymerase alpha subunit	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	C-terminal domain of RNA polymerase alpha subunit	8042964	3000519	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	C-terminal domain of RNA polymerase alpha subunit	8042964	3000519	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	C-terminal domain of RNA polymerase alpha subunit	8042964	3000519	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	C-terminal domain of RNA polymerase alpha subunit	8042964	3000519	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	C-terminal domain of RNA polymerase alpha subunit	8042964	3000519	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	C-terminal domain of RNA polymerase alpha subunit	8042964	3000519	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	C-terminal domain of RNA polymerase alpha subunit	8042964	3000519	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	C-terminal domain of RNA polymerase alpha subunit	8042964	3000519	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)
B	PF03118	e3k4gB1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF03118	ECOD (1.6)
F	PF03118	e3k4gF1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF03118	ECOD (1.6)
H	PF03118	e3k4gH1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF03118	ECOD (1.6)
A	PF03118	e3k4gA1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF03118	ECOD (1.6)
C	PF03118	e3k4gC1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF03118	ECOD (1.6)
D	PF03118	e3k4gD1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF03118	ECOD (1.6)
E	PF03118	e3k4gE1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF03118	ECOD (1.6)
G	PF03118	e3k4gG1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF03118	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
F	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
H	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
C	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
D	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
E	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
G	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF03118	Bacterial RNA polymerase, alpha chain C terminal domain (RNA_pol_A_CTD)	Bacterial RNA polymerase, alpha chain C terminal domain	The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. T ...	The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	DNA-directed RNA polymerase subunit alpha	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein binding DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein binding protein dimerization activity	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process primary metabolic process negative regulation of cellular biosynthetic process regulation of gene expression organic cyclic compound metabolic process biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process organic substance metabolic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of gene expression negative regulation of biosynthetic process cellular process positive regulation of cellular biosynthetic process regulation of DNA-templated transcription initiation DNA-templated transcription initiation cellular response to stimulus cellular response to stress response to stimulus response to stress cellular response to cell envelope stress organelle assembly cell projection organization non-membrane-bounded organelle assembly bacterial-type flagellum assembly cellular component biogenesis bacterial-type flagellum organization organelle organization cellular component assembly cell projection assembly nitrate assimilation oxoacid metabolic process organic acid metabolic process reactive nitrogen species metabolic process nitrogen cycle metabolic process small molecule metabolic process nitrate metabolic process regulation of DNA-templated transcription elongation DNA-templated transcription elongation cell aggregation biofilm formation aggregation of unicellular organisms submerged biofilm formation cell motility response to heat response to abiotic stimulus response to temperature stimulus bacterial-type flagellum-dependent cell motility archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility	protein-containing complex intracellular anatomical structure catalytic complex transferase complex cellular anatomical entity transferase complex, transferring phosphorus-containing groups cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex transferase complex cellular anatomical entity transferase complex, transferring phosphorus-containing groups cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex membrane membrane-bounded organelle transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D, E A, B, C, D, E, F, G, H	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.