1KU2

Crystal Structure of Thermus aquaticus RNA Polymerase Sigma Subunit Fragment Containing Regions 1.2 to 3.1

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)
A	d1ku2a1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	Sigma3 domain	Sigma factor SigA	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
A	d1ku2a2	All alpha proteins	Sigma2 domain of RNA polymerase sigma factors	Sigma2 domain of RNA polymerase sigma factors	Sigma2 domain of RNA polymerase sigma factors	Sigma factor SigA	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
B	d1ku2b1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	Sigma3 domain	Sigma factor SigA	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
B	d1ku2b2	All alpha proteins	Sigma2 domain of RNA polymerase sigma factors	Sigma2 domain of RNA polymerase sigma factors	Sigma2 domain of RNA polymerase sigma factors	Sigma factor SigA	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Sigma2 domain of RNA polymerase sigma factors	8032033	4003741	SCOP2 (2022-06-29)
A	SCOP2 Family	Sigma3 domain	8032032	4003497	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sigma2 domain of RNA polymerase sigma factors	8044411	3001393	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sigma factor domain-like	8044410	3000953	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Sigma factor domain-like	8044410	3000953	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sigma2 domain of RNA polymerase sigma factors	8044411	3001393	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)
A	PF04539	e1ku2A1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF04539	ECOD (1.6)
A	PF00140,PF04542	e1ku2A2	A: alpha complex topology	X: Sigma2 domain-like	H: Sigma2 domain of RNA polymerase sigma factors (From Topology)	T: Sigma2 domain of RNA polymerase sigma factors	F: PF00140,PF04542	ECOD (1.6)
B	PF04539	e1ku2B1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF04539	ECOD (1.6)
B	PF00140,PF04542	e1ku2B2	A: alpha complex topology	X: Sigma2 domain-like	H: Sigma2 domain of RNA polymerase sigma factors (From Topology)	T: Sigma2 domain of RNA polymerase sigma factors	F: PF00140,PF04542	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.1810	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
A	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)
B	1.20.120.1810	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
B	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF04539	Sigma-70 region 3 (Sigma70_r3)	Sigma-70 region 3	-	Family
A, B	PF00140	Sigma-70 factor, region 1.2 (Sigma70_r1_2)	Sigma-70 factor, region 1.2	-	Family
A, B	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	sigma factor sigA	DNA binding binding organic cyclic compound binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity sigma factor activity	cellular biosynthetic process cellular metabolic 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process cellular biosynthetic process cellular metabolic 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR007627	RNA polymerase sigma-70 region 2	Domain
A, B	IPR000943	RNA polymerase sigma-70	Domain
A, B	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
A, B	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
A, B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR012760	RNA polymerase sigma factor RpoD, C-terminal	Domain
A, B	IPR014284	RNA polymerase sigma-70 like domain	Domain
A, B	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
A, B	IPR007630	RNA polymerase sigma-70 region 4	Domain
A, B	IPR007624	RNA polymerase sigma-70 region 3	Domain
A, B	IPR028630	RNA polymerase sigma factor RpoD	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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.