3UMG | pdb_00003umg

Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase Rha0230

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)
H	d3umgh_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)
G	d3umgg_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)
F	d3umgf_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)
E	d3umge_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)
D	d3umgd_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)
C	d3umgc_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)
B	d3umgb_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)
A	d3umga_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	HAD_2	e3umgH1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)
G	HAD_2	e3umgG1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)
F	HAD_2	e3umgF1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)
E	HAD_2	e3umgE1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)
D	HAD_2	e3umgD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)
C	HAD_2	e3umgC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)
B	HAD_2	e3umgB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)
A	HAD_2	e3umgA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
H	1.10.150.240	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
G	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
G	1.10.150.240	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
F	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
F	1.10.150.240	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
E	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
E	1.10.150.240	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	1.10.150.240	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	1.10.150.240	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	1.10.150.240	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
A	1.10.150.240	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, E A, B, C, D, E, F, G, H	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, E A, B, C, D, E, F, G, H	Haloacid dehalogenase	(S)-2-haloacid dehalogenase activity hydrolase activity, acting on acid halide bonds hydrolase activity hydrolase activity, acting on acid halide bonds, in C-halide compounds catalytic activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006328	L-2-Haloacid dehalogenase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR051540	S-2-haloalkanoic acid dehalogenase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036412	HAD-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR023214	HAD superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006439	HAD hydrolase, subfamily IA	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.