1RXQ | pdb_00001rxq

YfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topology

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)
A	d1rxqa_	All alpha proteins	DinB/YfiT-like putative metalloenzymes	DinB/YfiT-like putative metalloenzymes	YfiT-like putative metal-dependent hydrolases	YfiT	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1rxqb_	All alpha proteins	DinB/YfiT-like putative metalloenzymes	DinB/YfiT-like putative metalloenzymes	YfiT-like putative metal-dependent hydrolases	YfiT	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d1rxqc_	All alpha proteins	DinB/YfiT-like putative metalloenzymes	DinB/YfiT-like putative metalloenzymes	YfiT-like putative metal-dependent hydrolases	YfiT	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d1rxqd_	All alpha proteins	DinB/YfiT-like putative metalloenzymes	DinB/YfiT-like putative metalloenzymes	YfiT-like putative metal-dependent hydrolases	YfiT	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	YfiT-like putative metal-dependent hydrolases	8026605	4002482	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DinB/YfiT-like putative metalloenzymes	8038984	3001308	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	DinB/YfiT-like putative metalloenzymes	8038984	3001308	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DinB/YfiT-like putative metalloenzymes	8038984	3001308	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DinB/YfiT-like putative metalloenzymes	8038984	3001308	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)
A	DinB_2	e1rxqA1	A: alpha bundles	X: YfiT-like putative metal-dependent hydrolases (From Topology)	H: YfiT-like putative metal-dependent hydrolases (From Topology)	T: YfiT-like putative metal-dependent hydrolases	F: DinB_2	ECOD (1.6)
B	DinB_2	e1rxqB1	A: alpha bundles	X: YfiT-like putative metal-dependent hydrolases (From Topology)	H: YfiT-like putative metal-dependent hydrolases (From Topology)	T: YfiT-like putative metal-dependent hydrolases	F: DinB_2	ECOD (1.6)
C	DinB_2	e1rxqC1	A: alpha bundles	X: YfiT-like putative metal-dependent hydrolases (From Topology)	H: YfiT-like putative metal-dependent hydrolases (From Topology)	T: YfiT-like putative metal-dependent hydrolases	F: DinB_2	ECOD (1.6)
D	DinB_2	e1rxqD1	A: alpha bundles	X: YfiT-like putative metal-dependent hydrolases (From Topology)	H: YfiT-like putative metal-dependent hydrolases (From Topology)	T: YfiT-like putative metal-dependent hydrolases	F: DinB_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.450	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	dinb family like domain	CATH (4.3.0)
B	1.20.120.450	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	dinb family like domain	CATH (4.3.0)
C	1.20.120.450	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	dinb family like domain	CATH (4.3.0)
D	1.20.120.450	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	dinb family like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF12867	DinB superfamily (DinB_2)	DinB superfamily	The DinB family are an uncharacterised family of potential enzymes. The structure of these proteins is composed of a four helix bundle [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	yfiT	hydrolase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	-	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR024775	DinB-like domain	Domain
A, B, C, D	IPR023774	Putative metal-dependent hydrolase YfiT	Family
A, B, C, D	IPR034660	DinB/YfiT-like putative metalloenzymes	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.