1L0O

Crystal Structure of the Bacillus stearothermophilus Anti-Sigma Factor SpoIIAB with the Sporulation Sigma Factor SigmaF

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d1l0oc_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	Sigma4 domain	SigmaF	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
A	d1l0oa_	Alpha and beta proteins (a+b)	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	Histidine kinase	Anti-sigma factor spoIIab	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
B	d1l0ob_	Alpha and beta proteins (a+b)	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	Histidine kinase	Anti-sigma factor spoIIab	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2 Family	Sigma4 domain	8028540	4003503	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Sigma factor domain-like	8040919	3000953	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	GHKL (Gyrase Hsp90 Histidine Kinase MutL) domain-like	8040207	3000091	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GHKL (Gyrase Hsp90 Histidine Kinase MutL) domain-like	8040207	3000091	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)
C	Sigma70_r3	e1l0oC1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r3	ECOD (1.6)
A	HATPase_c_2	e1l0oA1	A: a+b two layers	X: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like	H: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase (From Topology)	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: HATPase_c_2	ECOD (1.6)
B	HATPase_c_2	e1l0oB1	A: a+b two layers	X: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like	H: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase (From Topology)	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: HATPase_c_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	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)
A	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
B	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF04539	Sigma-70 region 3 (Sigma70_r3)	Sigma-70 region 3	-	Family
C	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
A, B	PF02518	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase (HATPase_c)	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase	This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	sigma factor	DNA binding binding organic cyclic compound binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity sigma factor activity	sporulation resulting in formation of a cellular spore developmental process anatomical structure morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development sporulation 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 sporulation resulting in formation of a cellular spore developmental process anatomical structure morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development sporulation 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	-
A, B	Anti-sigma F factor	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein serine kinase activity sigma factor antagonist activity transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity	phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process developmental process asexual sporulation reproductive process sporulation developmental process involved in reproduction asexual reproduction sporulation resulting in formation of a cellular spore anatomical structure morphogenesis phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process developmental process asexual sporulation reproductive process sporulation developmental process involved in reproduction asexual reproduction sporulation resulting in formation of a cellular spore anatomical structure morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development regulation of biological process regulation of developmental process negative regulation of sporulation resulting in formation of a cellular spore negative regulation of developmental process biological regulation negative regulation of biological process negative regulation of sporulation regulation of sporulation resulting in formation of a cellular spore regulation of sporulation	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR007627	RNA polymerase sigma-70 region 2	Domain
C	IPR000943	RNA polymerase sigma-70	Domain
C	IPR001387	Cro/C1-type helix-turn-helix domain	Domain
C	IPR014322	RNA polymerase sigma-B/F/G type	Family
C	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
C	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
C	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
C	IPR014284	RNA polymerase sigma-70 like domain	Domain
C	IPR007630	RNA polymerase sigma-70 region 4	Domain
C	IPR007624	RNA polymerase sigma-70 region 3	Domain
C	IPR014236	RNA polymerase sigma-F type	Family
A, B	IPR003594	Histidine kinase/HSP90-like ATPase	Domain
A, B	IPR010194	Anti-sigma F factor	Family
A, B	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	non-specific serine/threonine protein kinase M-CSA #760	The control of sporulation in some bacteria is controlled by sigma factors, one of which is sigma-F which triggers the cascade of gene expression in the forespore compartment of the sporulating cell. Control of sigma-F is by the SpoII proteins: SpoIIAB, which binds to sigma-F and thereby inactivates it; SpoIIAA, a non-enzymatic protein which is phosphorylated by SpoIIAB, thus inducing release of sigma-F; and SpoIIE, a phosphatase which returns SpoII-P to the dephosphorylated state. SpoIIAB has the same ATP-binding domain as other members of the GHKL superfamily. It phosphorylates the Ser 58 residue of SpoIIAA, using up ATP.	Defined by 3 residues: GLU:A-46ASN:A-50ARG:A-105 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif

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.