1VGX | pdb_00001vgx

Crystal structure of a autoinducer-2 synthesis protein

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	d1vgxb_	Alpha and beta proteins (a+b)	LuxS/MPP-like metallohydrolase	LuxS/MPP-like metallohydrolase	Autoinducer-2 production protein LuxS	Autoinducer-2 production protein LuxS	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
A	d1vgxa_	Alpha and beta proteins (a+b)	LuxS/MPP-like metallohydrolase	LuxS/MPP-like metallohydrolase	Autoinducer-2 production protein LuxS	Autoinducer-2 production protein LuxS	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8034124	3001831	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8034124	3001831	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	Peptidase_M16	e1vgxB1	A: alpha bundles	X: EGF-like	H: General secretion pathway protein M (EpsM) periplasmic domain-related	T: General secretion pathway protein M (EpsM) periplasmic domain-related	F: Peptidase_M16	ECOD (develop294)
A	Peptidase_M16	e1vgxA1	A: alpha bundles	X: EGF-like	H: General secretion pathway protein M (EpsM) periplasmic domain-related	T: General secretion pathway protein M (EpsM) periplasmic domain-related	F: Peptidase_M16	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.1360.80	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
A	3.30.1360.80	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02664	S-Ribosylhomocysteinase (LuxS) (LuxS)	S-Ribosylhomocysteinase (LuxS)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	S-ribosylhomocysteinase	carbon-sulfur lyase activity S-ribosylhomocysteine lyase activity lyase activity catalytic activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding	regulation of biological process response to stimulus signaling quorum sensing biological regulation cell-cell signaling detection of cell density detection of biotic stimulus response to biotic stimulus cell communication detection of stimulus cellular process oxoacid metabolic process sulfur amino acid metabolic process regulation of biological process response to stimulus signaling quorum sensing biological regulation cell-cell signaling detection of cell density detection of biotic stimulus response to biotic stimulus cell communication detection of stimulus cellular process oxoacid metabolic process sulfur amino acid metabolic process aspartate family amino acid biosynthetic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process metabolic compound salvage S-adenosylmethionine metabolic process sulfur compound metabolic process small molecule metabolic process L-methionine biosynthetic process S-adenosylmethionine cycle small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process methionine metabolic process L-amino acid metabolic process L-methionine salvage from S-adenosylmethionine proteinogenic amino acid metabolic process amino acid salvage amino acid biosynthetic process sulfur compound biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process L-methionine salvage sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR003815	S-ribosylhomocysteinase (LuxS)	Family
A, B	IPR011249	Metalloenzyme, LuxS/M16 peptidase-like	Homologous Superfamily
A, B	IPR037005	S-ribosylhomocysteinase (LuxS) superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	CSD	Parent Component: CYS RESID: AA0262 PSI-MOD : L-cysteine sulfinic acid MOD:00267

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.