4BIF | pdb_00004bif

Biochemical and structural characterisation of a novel manganese- dependent hydroxynitrile lyase from bacteria

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)
H	d4bifh_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Granulicella tundricola MP5ACTX9 ) [TaxId: 1198114 ],	SCOPe (2.08)
G	d4bifg_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Granulicella tundricola MP5ACTX9 ) [TaxId: 1198114 ],	SCOPe (2.08)
F	d4biff_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Granulicella tundricola MP5ACTX9 ) [TaxId: 1198114 ],	SCOPe (2.08)
E	d4bife_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Granulicella tundricola MP5ACTX9 ) [TaxId: 1198114 ],	SCOPe (2.08)
D	d4bifd_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Granulicella tundricola MP5ACTX9 ) [TaxId: 1198114 ],	SCOPe (2.08)
C	d4bifc_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Granulicella tundricola MP5ACTX9 ) [TaxId: 1198114 ],	SCOPe (2.08)
B	d4bifb_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Granulicella tundricola MP5ACTX9 ) [TaxId: 1198114 ],	SCOPe (2.08)
A	d4bifa_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Granulicella tundricola MP5ACTX9 ) [TaxId: 1198114 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	RmlC-like cupins	8089470	3001825	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RmlC-like cupins	8089470	3001825	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RmlC-like cupins	8089470	3001825	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RmlC-like cupins	8089470	3001825	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RmlC-like cupins	8089470	3001825	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RmlC-like cupins	8089470	3001825	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RmlC-like cupins	8089470	3001825	SCOP2B (2022-06-29)
A	SCOP2 Family	TM1287-like	8089469	4003968	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RmlC-like cupins	8089470	3001825	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	adh_short_C2	e4bifH1	A: a/b three-layered sandwiches	X: HAMP domain	H: Metalloproteases (zincins) catalytic domain	T: Metalloproteases (zincins) catalytic domain	F: adh_short_C2	ECOD (v294.1)
G	adh_short_C2	e4bifG1	A: a/b three-layered sandwiches	X: HAMP domain	H: Metalloproteases (zincins) catalytic domain	T: Metalloproteases (zincins) catalytic domain	F: adh_short_C2	ECOD (v294.1)
F	adh_short_C2	e4bifF1	A: a/b three-layered sandwiches	X: HAMP domain	H: Metalloproteases (zincins) catalytic domain	T: Metalloproteases (zincins) catalytic domain	F: adh_short_C2	ECOD (v294.1)
E	adh_short_C2	e4bifE1	A: a/b three-layered sandwiches	X: HAMP domain	H: Metalloproteases (zincins) catalytic domain	T: Metalloproteases (zincins) catalytic domain	F: adh_short_C2	ECOD (v294.1)
D	adh_short_C2	e4bifD1	A: a/b three-layered sandwiches	X: HAMP domain	H: Metalloproteases (zincins) catalytic domain	T: Metalloproteases (zincins) catalytic domain	F: adh_short_C2	ECOD (v294.1)
C	adh_short_C2	e4bifC1	A: a/b three-layered sandwiches	X: HAMP domain	H: Metalloproteases (zincins) catalytic domain	T: Metalloproteases (zincins) catalytic domain	F: adh_short_C2	ECOD (v294.1)
B	adh_short_C2	e4bifB1	A: a/b three-layered sandwiches	X: HAMP domain	H: Metalloproteases (zincins) catalytic domain	T: Metalloproteases (zincins) catalytic domain	F: adh_short_C2	ECOD (v294.1)
A	adh_short_C2	e4bifA1	A: a/b three-layered sandwiches	X: HAMP domain	H: Metalloproteases (zincins) catalytic domain	T: Metalloproteases (zincins) catalytic domain	F: adh_short_C2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
G	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
F	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
E	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
D	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
C	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
B	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
A	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	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	PF07883	Cupin domain (Cupin_2)	Cupin domain	This family represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel).	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	CUPIN 2 CONSERVED BARREL DOMAIN PROTEIN	mandelonitrile lyase activity lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR047263	Hydroxynitrile lyase-like, cupin domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR011051	RmlC-like cupin domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013096	Cupin 2, conserved barrel	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR014710	RmlC-like jelly roll fold	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.