1VHN | pdb_00001vhn

Crystal structure of a putative flavin oxidoreductase with flavin

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	d1vhna1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	FMN-linked oxidoreductases	Putative flavin oxidoreducatase TM0096	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d1vhna2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	FMN-linked oxidoreductases	8003352	4000080	SCOP2 (2022-06-29)
A	SCOP2 Family	Dus C-terminal domain-like	8056841	4007673	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FMN-linked oxidoreductases	8017570	3000014	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Dus C-terminal domain-like	8056842	3002362	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)
A	DHO_dh	e1vhnA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHO_dh	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	1.10.1200.80	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01207	Dihydrouridine synthase (Dus) (Dus)	Dihydrouridine synthase (Dus)	Members of this family catalyse the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the ...	Members of this family catalyse the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 (Swiss:Q9HGN6) from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 (Swiss:P53720) acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD [1]. Some family members may be targeted to the mitochondria and even have a role in mitochondria [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	putative flavin oxidoreductase	RNA binding binding tRNA binding nucleic acid binding oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA RNA dihydrouridine synthase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity tRNA dihydrouridine synthase activity flavin adenine dinucleotide binding RNA binding binding tRNA binding nucleic acid binding oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA RNA dihydrouridine synthase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity tRNA dihydrouridine synthase activity flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001269	tRNA-dihydrouridine synthase	Family
A	IPR018517	tRNA-dihydrouridine synthase, conserved site	Conserved Site
A	IPR004652	tRNA-dihydrouridine synthase DusB-like	Family
A	IPR035587	DUS-like, FMN-binding domain	Domain
A	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A	IPR024036	tRNA-dihydrouridine synthase, putative, C-terminal	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.