1DW9 | pdb_00001dw9

Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d1dw9c1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	Cyanase N-terminal domain	Cyanase N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1dw9c2	Alpha and beta proteins (a+b)	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1dw9d1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	Cyanase N-terminal domain	Cyanase N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1dw9d2	Alpha and beta proteins (a+b)	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d1dw9h1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	Cyanase N-terminal domain	Cyanase N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d1dw9h2	Alpha and beta proteins (a+b)	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I	d1dw9i1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	Cyanase N-terminal domain	Cyanase N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I	d1dw9i2	Alpha and beta proteins (a+b)	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J	d1dw9j1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	Cyanase N-terminal domain	Cyanase N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J	d1dw9j2	Alpha and beta proteins (a+b)	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1dw9a1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	Cyanase N-terminal domain	Cyanase N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1dw9a2	Alpha and beta proteins (a+b)	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1dw9b1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	Cyanase N-terminal domain	Cyanase N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1dw9b2	Alpha and beta proteins (a+b)	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1dw9e1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	Cyanase N-terminal domain	Cyanase N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1dw9e2	Alpha and beta proteins (a+b)	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d1dw9f1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	Cyanase N-terminal domain	Cyanase N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d1dw9f2	Alpha and beta proteins (a+b)	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d1dw9g1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	Cyanase N-terminal domain	Cyanase N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d1dw9g2	Alpha and beta proteins (a+b)	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	Cyanase C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Cyanase C-terminal domain	8035792	3001610	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8037199	3000119	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cyanase C-terminal domain	8035792	3001610	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8037199	3000119	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Cyanase C-terminal domain	8035792	3001610	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8037199	3000119	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Cyanase C-terminal domain	8035792	3001610	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8037199	3000119	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Cyanase C-terminal domain	8035792	3001610	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8037199	3000119	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cyanase C-terminal domain	8035792	3001610	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8037199	3000119	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cyanase C-terminal domain	8035792	3001610	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8037199	3000119	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Cyanase C-terminal domain	8035792	3001610	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8037199	3000119	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Cyanase C-terminal domain	8035792	3001610	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8037199	3000119	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Cyanase C-terminal domain	8035792	3001610	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8037199	3000119	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)
C	PRK02866	e1dw9C1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PRK02866	ECOD (1.6)
C	Cyanate_lyase	e1dw9C2	A: a+b duplicates or obligate multimers	X: MinE-like	H: Cyanase C-terminal domain (From Topology)	T: Cyanase C-terminal domain	F: Cyanate_lyase	ECOD (1.6)
D	PRK02866	e1dw9D1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PRK02866	ECOD (1.6)
D	Cyanate_lyase	e1dw9D2	A: a+b duplicates or obligate multimers	X: MinE-like	H: Cyanase C-terminal domain (From Topology)	T: Cyanase C-terminal domain	F: Cyanate_lyase	ECOD (1.6)
H	PRK02866	e1dw9H1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PRK02866	ECOD (1.6)
H	Cyanate_lyase	e1dw9H2	A: a+b duplicates or obligate multimers	X: MinE-like	H: Cyanase C-terminal domain (From Topology)	T: Cyanase C-terminal domain	F: Cyanate_lyase	ECOD (1.6)
I	PRK02866	e1dw9I1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PRK02866	ECOD (1.6)
I	Cyanate_lyase	e1dw9I2	A: a+b duplicates or obligate multimers	X: MinE-like	H: Cyanase C-terminal domain (From Topology)	T: Cyanase C-terminal domain	F: Cyanate_lyase	ECOD (1.6)
J	PRK02866	e1dw9J1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PRK02866	ECOD (1.6)
J	Cyanate_lyase	e1dw9J2	A: a+b duplicates or obligate multimers	X: MinE-like	H: Cyanase C-terminal domain (From Topology)	T: Cyanase C-terminal domain	F: Cyanate_lyase	ECOD (1.6)
A	PRK02866	e1dw9A1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PRK02866	ECOD (1.6)
A	Cyanate_lyase	e1dw9A2	A: a+b duplicates or obligate multimers	X: MinE-like	H: Cyanase C-terminal domain (From Topology)	T: Cyanase C-terminal domain	F: Cyanate_lyase	ECOD (1.6)
B	PRK02866	e1dw9B1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PRK02866	ECOD (1.6)
B	Cyanate_lyase	e1dw9B2	A: a+b duplicates or obligate multimers	X: MinE-like	H: Cyanase C-terminal domain (From Topology)	T: Cyanase C-terminal domain	F: Cyanate_lyase	ECOD (1.6)
E	PRK02866	e1dw9E1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PRK02866	ECOD (1.6)
E	Cyanate_lyase	e1dw9E2	A: a+b duplicates or obligate multimers	X: MinE-like	H: Cyanase C-terminal domain (From Topology)	T: Cyanase C-terminal domain	F: Cyanate_lyase	ECOD (1.6)
F	PRK02866	e1dw9F1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PRK02866	ECOD (1.6)
F	Cyanate_lyase	e1dw9F2	A: a+b duplicates or obligate multimers	X: MinE-like	H: Cyanase C-terminal domain (From Topology)	T: Cyanase C-terminal domain	F: Cyanate_lyase	ECOD (1.6)
G	PRK02866	e1dw9G1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PRK02866	ECOD (1.6)
G	Cyanate_lyase	e1dw9G2	A: a+b duplicates or obligate multimers	X: MinE-like	H: Cyanase C-terminal domain (From Topology)	T: Cyanase C-terminal domain	F: Cyanate_lyase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
C	3.30.1160.10	Alpha Beta	2-Layer Sandwich	Cyanate Lyase	Chain: A, domain 2	CATH (4.3.0)
D	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
D	3.30.1160.10	Alpha Beta	2-Layer Sandwich	Cyanate Lyase	Chain: A, domain 2	CATH (4.3.0)
H	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
H	3.30.1160.10	Alpha Beta	2-Layer Sandwich	Cyanate Lyase	Chain: A, domain 2	CATH (4.3.0)
I	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
I	3.30.1160.10	Alpha Beta	2-Layer Sandwich	Cyanate Lyase	Chain: A, domain 2	CATH (4.3.0)
J	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
J	3.30.1160.10	Alpha Beta	2-Layer Sandwich	Cyanate Lyase	Chain: A, domain 2	CATH (4.3.0)
A	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
A	3.30.1160.10	Alpha Beta	2-Layer Sandwich	Cyanate Lyase	Chain: A, domain 2	CATH (4.3.0)
B	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
B	3.30.1160.10	Alpha Beta	2-Layer Sandwich	Cyanate Lyase	Chain: A, domain 2	CATH (4.3.0)
E	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
E	3.30.1160.10	Alpha Beta	2-Layer Sandwich	Cyanate Lyase	Chain: A, domain 2	CATH (4.3.0)
F	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
F	3.30.1160.10	Alpha Beta	2-Layer Sandwich	Cyanate Lyase	Chain: A, domain 2	CATH (4.3.0)
G	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
G	3.30.1160.10	Alpha Beta	2-Layer Sandwich	Cyanate Lyase	Chain: A, domain 2	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, I, J	PF02560	Cyanate lyase C-terminal domain (Cyanate_lyase)	Cyanate lyase C-terminal domain	Cyanate lyase (also known as cyanase) EC:4.2.1.104 is responsible for the hydrolysis of cyanate, allowing organisms that possess the enzyme to overcome the toxicity of environmental cyanate. This enzyme is composed of two domains, an N-terminal helix ...	Cyanate lyase (also known as cyanase) EC:4.2.1.104 is responsible for the hydrolysis of cyanate, allowing organisms that possess the enzyme to overcome the toxicity of environmental cyanate. This enzyme is composed of two domains, an N-terminal helix-turn-helix and this structurally unique C-terminal domain [2].	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	PF21291	Cyanate hydratase, N-terminal (CYNS_N)	Cyanate hydratase, N-terminal	Cyanate hydratase (also known as cyanate lyase) catalyses the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide, allowing the host organisms to overcome the toxicity of environmental cyanate [1-4]. It consists of an N-termin ...	Cyanate hydratase (also known as cyanate lyase) catalyses the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide, allowing the host organisms to overcome the toxicity of environmental cyanate [1-4]. It consists of an N-terminal five-helix bundle domain that shows structural similarity to DNA-binding HTH domains and a C-terminal catalytic domain, which has a unique fold [4].	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, I, J	CYANATE LYASE	DNA binding binding nucleic acid binding lyase activity cyanate hydratase activity catalytic activity carbon-nitrogen lyase activity	catabolic process cyanate metabolic process metabolic process cellular process small molecule metabolic process cyanate catabolic process organic acid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR036581	Cyanate lyase, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR008076	Cyanate hydratase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR003712	Cyanate lyase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR048564	Cyanate hydratase, N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR010982	Lambda repressor-like, DNA-binding domain superfamily	Homologous Superfamily

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

Chains	Enzyme Name	Description	Catalytic Residues
A, D	cyanase M-CSA #845	Cyanate lyase activity is present in some but not all bacteria. The enzyme detoxifies the cyanate ion, which reacts with nucleophilic groups of proteins. The enzyme is a decamer with unusual 5/2 (D2) symmetry, forming a pentamer of dimers. The active site is dyadic and made up of residues from two adjacent dimers. There are 5 active sites per decamer. The protein fold is unique but shows some similarity to DNA binding proteins such as 434 repressor, but the enzyme is not thought to bind DNA in vivo.	Defined by 3 residues: SER:A-122ARG:D-96GLU:D-99 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.3.99.1 (PDB Primary Data) Search M-CSA Motif + EC 4.3.99.1 EC: 4.2.1.104 (UniProt) Search M-CSA Motif + EC 4.2.1.104