4QIC

Co-Crystal Structure of Anti-anti-sigma factor PhyR complexed with Anti-sigma factor NepR from Bartonella quintana

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Sigma70_r4_2_1	e4qicA3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r4_2_1	ECOD (1.6)
A	PRK09191	e4qicA2	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: PRK09191	ECOD (1.6)
A	Response_reg	e4qicA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Response_reg	ECOD (1.6)
C	Sigma70_r4_2_1	e4qicC1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r4_2_1	ECOD (1.6)
C	PRK09191	e4qicC2	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: PRK09191	ECOD (1.6)
C	Response_reg	e4qicC3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Response_reg	ECOD (1.6)
B	EUF08787	e4qicB1	A: extended segments	X: Anti sigma factor NepR-related (From Topology)	H: Anti sigma factor NepR-related (From Topology)	T: Anti sigma factor NepR-related	F: EUF08787	ECOD (1.6)
D	EUF08787	e4qicD1	A: extended segments	X: Anti sigma factor NepR-related (From Topology)	H: Anti sigma factor NepR-related (From Topology)	T: Anti sigma factor NepR-related	F: EUF08787	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.140.160	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
C	1.20.140.160	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
C	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00072	Response regulator receiver domain (Response_reg)	Response regulator receiver domain	This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.	Domain
A, C	PF08281	Sigma-70, region 4 (Sigma70_r4_2)	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].	Domain
B, D	PF18557	Anti-sigma factor NepR (NepR)	Anti-sigma factor NepR	The general stress response sigma factor in alphaproteobacteria, sigma EcfG is inactivated by the anti-sigma factor NepR, which is itself regulated by the response regulator PhyR. NepR forms two helices that extend over the surface of the PhyR subdom ...	The general stress response sigma factor in alphaproteobacteria, sigma EcfG is inactivated by the anti-sigma factor NepR, which is itself regulated by the response regulator PhyR. NepR forms two helices that extend over the surface of the PhyR subdomains. Homology modeling and comparative analysis of NepR, PhyR and sigmaEcfG mutants indicate that NepR contacts both proteins with the same determinants, showing sigma factor mimicry at the atomic level. This entry represents NepR domains found in alphaproteobacteria [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Sensory transduction regulatory protein, Anti-anti-sigma factor PhyR	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 cellular response to stimulus regulation of biological process phosphorelay signal transduction system regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication signal transduction	-
B, D	Anti-sigma factor NepR	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR014605	Signal transduction response regulator PhyR-like, alphaproteobacteria	Family
A, C	IPR013249	RNA polymerase sigma factor 70, region 4 type 2	Domain
A, C	IPR011006	CheY-like superfamily	Homologous Superfamily
A, C	IPR001789	Signal transduction response regulator, receiver domain	Domain
A, C	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
B, D	IPR041649	Anti-sigma factor NepR	Domain

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.