4I9G

Crystal structure of glycerol phosphate phosphatase Rv1692 from Mycobacterium tuberculosis in complex with magnesium

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	PF18407	e4i9gA1	A: a+b three layers	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat) (From Topology)	T: Acyl-CoA N-acyltransferases (Nat)	F: PF18407	ECOD (1.6)
A	F_UNCLASSIFIED	e4i9gA2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF13242	e4i9gA3	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: PF13242	ECOD (1.6)
B	PF18407	e4i9gB1	A: a+b three layers	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat) (From Topology)	T: Acyl-CoA N-acyltransferases (Nat)	F: PF18407	ECOD (1.6)
B	F_UNCLASSIFIED	e4i9gB2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF13242	e4i9gB3	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: PF13242	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
A	3.30.300.290	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
B	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
B	3.30.300.290	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00702	haloacid dehalogenase-like hydrolase (Hydrolase)	haloacid dehalogenase-like hydrolase	This family is structurally different from the alpha/beta hydrolase family (Pfam:PF00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted fo ...	This family is structurally different from the alpha/beta hydrolase family (Pfam:PF00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of Swiss:P24069. The rest of the fold is composed of the core alpha/beta domain [1]. Those members with the characteristic DxD triad at the N-terminus are probably phosphatidylglycerolphosphate (PGP) phosphatases involved in cardiolipin biosynthesis in the mitochondria [2].	Domain
A, B	PF18407	GCN5-related N-acetyltransferase like domain (GNAT_like)	GCN5-related N-acetyltransferase like domain	This is a domain with a GCN5-related N-acetyltransferase (GNAT) fold which can be found in Rv1692 phophatases. Crystal structure of Rv1692 indicates that this C-temrinal extension, which is absent in other characterized HADSF members, resembles a sma ...	This is a domain with a GCN5-related N-acetyltransferase (GNAT) fold which can be found in Rv1692 phophatases. Crystal structure of Rv1692 indicates that this C-temrinal extension, which is absent in other characterized HADSF members, resembles a small GCN5-related N-acetyltransferase (GNAT) fold. Furthermore, it is fused to the HADSF catalytic domain Pfam:PF13242 . Functional studies indicate that this GNAT region is not likely to be involved in acetyl group transfer using AcCoA and SucCoA, it could nonetheless be a regulatory domain. Furthermore, it is suggested that this GNAT domain is required for the solubility of the HADSF fold of Rv1692 and is potentially needed for the structural integrity of this enzyme [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Glycerol 3-phosphate phosphatase	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding magnesium ion binding manganese ion binding identical protein binding protein binding protein homodimerization activity protein dimerization activity phosphoric ester hydrolase activity cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding magnesium ion binding manganese ion binding identical protein binding protein binding protein homodimerization activity protein dimerization activity phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity glycerol-1-phosphatase activity	carbohydrate metabolic process polyol metabolic process organic substance metabolic process alditol metabolic process organic hydroxy compound metabolic process primary metabolic process metabolic process alcohol metabolic process small molecule metabolic process glycerol metabolic process lipid catabolic process catabolic process phospholipid catabolic process cellular metabolic process carbohydrate metabolic process polyol metabolic process organic substance metabolic process alditol metabolic process organic hydroxy compound metabolic process primary metabolic process metabolic process alcohol metabolic process small molecule metabolic process glycerol metabolic process lipid catabolic process catabolic process phospholipid catabolic process cellular metabolic process glycerophospholipid metabolic process glycerolipid catabolic process organophosphate catabolic process cellular lipid catabolic process cellular catabolic process phospholipid metabolic process organophosphate metabolic process cellular lipid metabolic process phosphate-containing compound metabolic process glycerophospholipid catabolic process cellular process glycerolipid metabolic process phosphorus metabolic process organic substance catabolic process lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036412	HAD-like superfamily	Homologous Superfamily
A, B	IPR023214	HAD superfamily	Homologous Superfamily
A, B	IPR041065	GCN5-related N-acetyltransferase-like domain	Domain
A, B	IPR006357	HAD-superfamily hydrolase, subfamily IIA	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.