6PUQ

1.56 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase Tyw1 in complex with FMN

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00258	e6puqA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: Flavoproteins	F: PF00258	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00258	Flavodoxin (Flavodoxin_1)	Flavodoxin	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Wybutosine biosynthesis protein Tyw1	binding nucleotide binding FMN binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxo-acid-lyase activity catalytic activity, acting on RNA tRNA-4-demethylwyosine synthase activity binding nucleotide binding FMN binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxo-acid-lyase activity catalytic activity, acting on RNA tRNA-4-demethylwyosine synthase activity catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA lyase activity catalytic activity carbon-carbon lyase activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding electron transfer activity cation binding metal ion binding	glycosyl compound metabolic process wybutosine metabolic process cellular biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing carbohydrate derivative biosynthetic process organonitrogen compound metabolic process glycosyl compound biosynthetic process glycosyl compound metabolic process wybutosine metabolic process cellular biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing carbohydrate derivative biosynthetic process organonitrogen compound metabolic process glycosyl compound biosynthetic process wybutosine biosynthetic process cellular metabolic process tRNA modification primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process organic cyclic compound metabolic process RNA modification biosynthetic process macromolecule modification nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process	membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR007197	Radical SAM	Domain
A	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A	IPR013917	tRNA wybutosine-synthesis	Domain
A	IPR008254	Flavodoxin/nitric oxide synthase	Domain
A	IPR034556	S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase	Family
A	IPR001226	Flavodoxin, conserved site	Conserved Site
A	IPR029039	Flavoprotein-like superfamily	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 R01GM133198.