2DD5 | pdb_00002dd5

Thiocyanate hydrolase (SCNase) from Thiobacillus thioparus native holo-enzyme

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	Nitrile hydratase alpha chain	8077353	3000945	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Nitrile hydratase alpha chain	8077353	3000945	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Nitrile hydratase alpha chain	8077353	3000945	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nitrile hydratase alpha chain	8077353	3000945	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)
L	NHase_alpha	e2dd5L1	A: a+b complex topology	X: Nitrile hydratase alpha chain (From Topology)	H: Nitrile hydratase alpha chain (From Topology)	T: Nitrile hydratase alpha chain	F: NHase_alpha	ECOD (1.6)
I	NHase_alpha	e2dd5I1	A: a+b complex topology	X: Nitrile hydratase alpha chain (From Topology)	H: Nitrile hydratase alpha chain (From Topology)	T: Nitrile hydratase alpha chain	F: NHase_alpha	ECOD (1.6)
F	NHase_alpha	e2dd5F1	A: a+b complex topology	X: Nitrile hydratase alpha chain (From Topology)	H: Nitrile hydratase alpha chain (From Topology)	T: Nitrile hydratase alpha chain	F: NHase_alpha	ECOD (1.6)
C	NHase_alpha	e2dd5C1	A: a+b complex topology	X: Nitrile hydratase alpha chain (From Topology)	H: Nitrile hydratase alpha chain (From Topology)	T: Nitrile hydratase alpha chain	F: NHase_alpha	ECOD (1.6)
K	NHase_beta_N	e2dd5K1	A: alpha arrays	X: Nitrile hydratase subunit beta N-termial domain (From Topology)	H: Nitrile hydratase subunit beta N-termial domain (From Topology)	T: Nitrile hydratase subunit beta N-termial domain	F: NHase_beta_N	ECOD (1.6)
H	NHase_beta_N	e2dd5H1	A: alpha arrays	X: Nitrile hydratase subunit beta N-termial domain (From Topology)	H: Nitrile hydratase subunit beta N-termial domain (From Topology)	T: Nitrile hydratase subunit beta N-termial domain	F: NHase_beta_N	ECOD (1.6)
E	NHase_beta_N	e2dd5E1	A: alpha arrays	X: Nitrile hydratase subunit beta N-termial domain (From Topology)	H: Nitrile hydratase subunit beta N-termial domain (From Topology)	T: Nitrile hydratase subunit beta N-termial domain	F: NHase_beta_N	ECOD (1.6)
B	NHase_beta_N	e2dd5B1	A: alpha arrays	X: Nitrile hydratase subunit beta N-termial domain (From Topology)	H: Nitrile hydratase subunit beta N-termial domain (From Topology)	T: Nitrile hydratase subunit beta N-termial domain	F: NHase_beta_N	ECOD (1.6)
J	NHase_beta_C	e2dd5J1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: NHase_beta_C	ECOD (1.6)
G	NHase_beta_C	e2dd5G1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: NHase_beta_C	ECOD (1.6)
D	NHase_beta_C	e2dd5D1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: NHase_beta_C	ECOD (1.6)
A	NHase_beta_C	e2dd5A1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: NHase_beta_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	3.90.330.10	Alpha Beta	Alpha-Beta Complex	Nitrile Hydratase	Chain A	CATH (4.3.0)
I	3.90.330.10	Alpha Beta	Alpha-Beta Complex	Nitrile Hydratase	Chain A	CATH (4.3.0)
F	3.90.330.10	Alpha Beta	Alpha-Beta Complex	Nitrile Hydratase	Chain A	CATH (4.3.0)
C	3.90.330.10	Alpha Beta	Alpha-Beta Complex	Nitrile Hydratase	Chain A	CATH (4.3.0)
K	1.10.472.20	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
H	1.10.472.20	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
E	1.10.472.20	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
B	1.10.472.20	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
J	2.30.30.50	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
G	2.30.30.50	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
D	2.30.30.50	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
A	2.30.30.50	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F, I, L	PF02979	Nitrile hydratase, alpha chain (NHase_alpha)	Nitrile hydratase, alpha chain		Domain
B, E, H, K	PF21006	Nitrile hydratase beta subunit, N-terminal (NHase_beta_N)	Nitrile hydratase beta subunit, N-terminal	Nitrile hydratases (NHases) EC:4.2.1.84 are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as ...	Nitrile hydratases (NHases) EC:4.2.1.84 are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit [1]. Beta subunit consists of an N-terminal helical domain, represented in this entry, and a C-terminal SH3-like domain (Pfam:PF02211) [2,3]. Thiocyanate hydrolase (SCNase) is a member of the NHase family and comprises alpha, beta and gamma subunits, which share amino acid sequence similarities with NHase beta subunit C-terminal, beta subunit N-terminal and NHase alpha subunit, respectively [3].	Domain
A, D, G, J	PF02211	Nitrile hydratase beta subunit, C-terminal (NHase_beta_C)	Nitrile hydratase beta subunit, C-terminal	Nitrile hydratases (NHase) EC:4.2.1.84 are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as ...	Nitrile hydratases (NHase) EC:4.2.1.84 are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit [1]. Beta subunit consists of an N-terminal helical domain and a C-terminal SH3-like domain (represented in this entry) [2,3]. Thiocyanate hydrolase (SCNase) is a member of the NHase family, comprises alpha, beta and gamma subunits which share amino acid sequence similarities with NHase beta subunit C-terminal, beta subunit N-terminal and NHase alpha subunit, respectively [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F, I, L	Thiocyanate hydrolase gamma subunit	cation binding transition metal ion binding ion binding binding metal ion binding small molecule binding thiocyanate hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in nitriles hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	cellular response to stimulus catabolic process response to stimulus thiocyanate catabolic process cellular response to xenobiotic stimulus organic acid metabolic process xenobiotic catabolic process xenobiotic metabolic process response to xenobiotic stimulus sulfur compound catabolic process cellular response to chemical stimulus thiocyanate metabolic process response to chemical small molecule metabolic process cellular response to stimulus catabolic process response to stimulus thiocyanate catabolic process cellular response to xenobiotic stimulus organic acid metabolic process xenobiotic catabolic process xenobiotic metabolic process response to xenobiotic stimulus sulfur compound catabolic process cellular response to chemical stimulus thiocyanate metabolic process response to chemical small molecule metabolic process metabolic process cellular process sulfur compound metabolic process small molecule catabolic process	-
B, E, H, K	Thiocyanate hydrolase beta subunit	thiocyanate hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in nitriles hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	cellular response to stimulus catabolic process response to stimulus thiocyanate catabolic process cellular response to xenobiotic stimulus organic acid metabolic process xenobiotic catabolic process xenobiotic metabolic process response to xenobiotic stimulus sulfur compound catabolic process cellular response to chemical stimulus thiocyanate metabolic process response to chemical small molecule metabolic process cellular response to stimulus catabolic process response to stimulus thiocyanate catabolic process cellular response to xenobiotic stimulus organic acid metabolic process xenobiotic catabolic process xenobiotic metabolic process response to xenobiotic stimulus sulfur compound catabolic process cellular response to chemical stimulus thiocyanate metabolic process response to chemical small molecule metabolic process metabolic process cellular process sulfur compound metabolic process small molecule catabolic process	-
A, D, G, J	Thiocyanate hydrolase alpha subunit	thiocyanate hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in nitriles hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	cellular response to stimulus catabolic process response to stimulus thiocyanate catabolic process cellular response to xenobiotic stimulus organic acid metabolic process xenobiotic catabolic process xenobiotic metabolic process response to xenobiotic stimulus sulfur compound catabolic process cellular response to chemical stimulus thiocyanate metabolic process response to chemical small molecule metabolic process cellular response to stimulus catabolic process response to stimulus thiocyanate catabolic process cellular response to xenobiotic stimulus organic acid metabolic process xenobiotic catabolic process xenobiotic metabolic process response to xenobiotic stimulus sulfur compound catabolic process cellular response to chemical stimulus thiocyanate metabolic process response to chemical small molecule metabolic process metabolic process cellular process sulfur compound metabolic process small molecule catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F, I, L	IPR004232	Nitrile hydratase alpha/Thiocyanate hydrolase gamma	Domain
C, F, I, L	IPR036648	Nitrile hydratase alpha /Thiocyanate hydrolase gamma superfamily	Homologous Superfamily
C, F, I, L	IPR023900	Nitrile hydratase alpha subunit /Thiocyanate hydrolase gamma subunit	Family
C, F, I, L	IPR023901	Thiocyanate hydrolase, gamma subunit	Family
B, E, H, K	IPR049054	Nitrile hydratase beta subunit-like, N-terminal domain	Domain
B, E, H, K	IPR008990	Electron transport accessory-like domain superfamily	Homologous Superfamily
B, E, H, K	IPR042262	Nitrile hydratase beta subunit, N-terminal	Homologous Superfamily
A, D, G, J	IPR008990	Electron transport accessory-like domain superfamily	Homologous Superfamily
A, D, G, J	IPR024690	Nitrile hydratase beta subunit domain	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, F, I, L	CSD	Parent Component: CYS RESID: AA0262 PSI-MOD : L-cysteine sulfinic acid MOD:00267
C, F, I, L	CSO	Parent Component: CYS RESID: AA0262 , AA0205 PSI-MOD : L-cysteine sulfinic acid MOD:00267 , L-cysteine sulfenic acid MOD:00210

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
B, C	thiocyanate hydrolase M-CSA #284	Thiocyanate hydrolase is a cobalt-containing metalloenzyme with a cysteine-sulphinic acid ligand that hydrolyses thiocyanate to carbonyl sulphide and ammonia. The enzyme from Thiobacillus thioparus catalyses the first step in the degradation of thiocyanate. Structural studies show all three chains to surround the active site, with positive side chains projecting towards the metal centre from each of them, stabilising the negatively charged substrate and product [PMID:17222425].	Defined by 5 residues: TYR:B-108CYS:C-128CYS:C-131SER:C-132CYS:C-133 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.5.5.8 (PDB Primary Data) Search M-CSA Motif + EC 3.5.5.8

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.