1VB6 | pdb_00001vb6

Crystal Structure of the heme PAS sensor domain of Ec DOS (oxygen-bound form)

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)
B	d1vb6b_	Alpha and beta proteins (a+b)	Profilin-like	PYP-like sensor domain (PAS domain)	Heme-binding PAS domain	Direct oxygen sensor protein, DOS	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d1vb6a_	Alpha and beta proteins (a+b)	Profilin-like	PYP-like sensor domain (PAS domain)	Heme-binding PAS domain	Direct oxygen sensor protein, DOS	(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	PYP-like sensor domain (PAS domain)	8033105	3000471	SCOP2B (2022-06-29)
A	SCOP2 Family	Heme-binding PAS domain	8020725	4001866	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PYP-like sensor domain (PAS domain)	8033105	3000471	SCOP2 (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		e1vb6B1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: tRNA-synt_2	F:	ECOD (20:10:01)
A		e1vb6A1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: tRNA-synt_2	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)
A	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF13426	PAS domain (PAS_9)	PAS domain	This domain is found in many signalling proteins in which it functions as a sensor domain. It recognises FMN, Zn(II), FAD and riboflavin (MAtilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Heme pas sensor protein	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity molecular sensor activity molecular function regulator activity oxygen sensor activity tetrapyrrole binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity molecular sensor activity molecular function regulator activity oxygen sensor activity tetrapyrrole binding heme binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity cyclic-guanylate-specific phosphodiesterase activity hydrolase activity catalytic activity	regulation of biological process cell aggregation regulation of cellular process biofilm formation regulation of single-species biofilm formation biological process involved in intraspecies interaction between organisms biological regulation cellular process single-species biofilm formation aggregation of unicellular organisms response to stimulus response to oxygen levels response to abiotic stimulus	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000014	PAS domain	Domain
A, B	IPR000160	GGDEF domain	Domain
A, B	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B	IPR035965	PAS domain superfamily	Homologous Superfamily
A, B	IPR001610	PAC motif	Repeat
A, B	IPR000700	PAS-associated, C-terminal	Domain
A, B	IPR012226	Diguanylate cyclase/phosphodiesterase	Family
A, B	IPR001633	EAL domain	Domain
A, B	IPR052155	Bacterial biofilm regulation/maintenance	Family
A, B	IPR035919	EAL domain superfamily	Homologous Superfamily
A, B	IPR029787	Nucleotide cyclase	Homologous Superfamily

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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.