3UXJ | pdb_00003uxj

Crystal Structure of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with NADP and PreQ0

External Resource: Annotation

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: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	CagX	e3uxjA1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: CagX	ECOD (v294.1)
B	CagX	e3uxjB1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: CagX	ECOD (v294.1)
D	CagX	e3uxjD1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: CagX	ECOD (v294.1)
C	CagX	e3uxjC1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: CagX	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1130.10	Alpha Beta	2-Layer Sandwich	GTP Cyclohydrolase I, domain 2	GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain	CATH (4.3.0)
B	3.30.1130.10	Alpha Beta	2-Layer Sandwich	GTP Cyclohydrolase I, domain 2	GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain	CATH (4.3.0)
D	3.30.1130.10	Alpha Beta	2-Layer Sandwich	GTP Cyclohydrolase I, domain 2	GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain	CATH (4.3.0)
C	3.30.1130.10	Alpha Beta	2-Layer Sandwich	GTP Cyclohydrolase I, domain 2	GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF14819	Nitrile reductase, 7-cyano-7-deazaguanine-reductase N-term (QueF_N)	Nitrile reductase, 7-cyano-7-deazaguanine-reductase N-term	The QueF monomer is made up of two ferredoxin-like domains aligned together with their beta-sheets that have additional embellishments. This subunit is composed of a three-stranded beta-sheet and two alpha-helices. QueF reduces a nitrile bond to a pr ...	The QueF monomer is made up of two ferredoxin-like domains aligned together with their beta-sheets that have additional embellishments. This subunit is composed of a three-stranded beta-sheet and two alpha-helices. QueF reduces a nitrile bond to a primary amine. The two monomer units together create suitable substrate-binding pockets [1].	Domain
A, B, C, D	PF14489	QueF-like protein (QueF)	QueF-like protein	This protein is involved in the biosynthesis of queuosine. In some proteins this domain appears to be fused to Pfam:PF06508.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	NADPH-dependent 7-cyano-7-deazaguanine reductase	oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors preQ1 synthase activity oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-NH group of donors catalytic activity	tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA queuosine(34) biosynthetic process tRNA wobble guanine modification tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA queuosine(34) biosynthetic process tRNA wobble guanine modification tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification metabolic process cellular process tRNA wobble base modification macromolecule metabolic process RNA processing	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR029500	NADPH-dependent 7-cyano-7-deazaguanine reductase QueF	Domain
A, B, C, D	IPR029139	NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal	Domain
A, B, C, D	IPR050084	NADPH-dependent 7-cyano-7-deazaguanine reductase	Family
A, B, C, D	IPR016428	NADPH-dependent 7-cyano-7-deazaguanine reductase, QueF type 2	Family
A, B, C, D	IPR043133	GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase	Homologous Superfamily

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

Chains	Enzyme Name	Description	Catalytic Residues
A	NADPH-dependent 7-cyano-7-deazaguanine reductase M-CSA #967	First discovered from the biosynthetic pathway of queuosine, QueF nitrile reductase is part of the tRNA biosynthetic pathway in the cytosol of bacteria. The role of QueF in this pathway is to catalyse the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ₀) to 7-aminomethyl-7-deazaguanine (preQ₁) by a unique four-electron reduction of nitrile to amine. This pathway is crucial for the pathogenicity of bacteria and has the potential to be used in industrial catalysis of organic compounds.	Defined by 5 residues: CYS:A-197 [auth A-194]THR:A-200 [auth A-197]ASP:A-204 [auth A-201]HIS:A-236 [auth A-233]GLU:A-237 [auth A-234] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.7.1.13 (PDB Primary Data) Search M-CSA Motif + EC 1.7.1.13

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.

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