3M1Y | pdb_00003m1y

Crystal Structure of a Phosphoserine phosphatase (SerB) from Helicobacter pylori

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
A	d3m1ya1	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
A	d3m1ya2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
B	d3m1yb_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
C	d3m1yc1	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
C	d3m1yc3	Artifacts	Tags	Tags	Tags	C-terminal Tags	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
C	d3m1yc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
D	d3m1yd1	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
D	d3m1yd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	HAD	e3m1yA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD	ECOD (1.6)
B	HAD	e3m1yB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD	ECOD (1.6)
C	HAD	e3m1yC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD	ECOD (1.6)
D	HAD	e3m1yD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD	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	1.10.150.210	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	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	1.10.150.210	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
C	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
C	1.10.150.210	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
D	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
D	1.10.150.210	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Phosphoserine phosphatase (SerB)	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity L-phosphoserine phosphatase activity catalytic activity	serine family amino acid metabolic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process L-serine metabolic process L-serine biosynthetic process serine family amino acid metabolic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process L-serine metabolic process L-serine biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR050582	HAD-like hydrolase superfamily, SerB	Family
A, B, C, D	IPR036412	HAD-like superfamily	Homologous Superfamily
A, B, C, D	IPR023214	HAD superfamily	Homologous Superfamily
A, B, C, D	IPR004469	Phosphoserine phosphatase	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 R01GM157729.