6PUP | pdb_00006pup

1.9 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	CSD	e6pupA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: CSD	ECOD (v294.1)

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	FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide 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 FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide 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 cation binding S-adenosyl-L-methionine binding sulfur compound binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding electron transfer activity metal ion binding	RNA metabolic process carbohydrate derivative metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing carbohydrate derivative biosynthetic process glycosyl compound biosynthetic process wybutosine biosynthetic process tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process RNA metabolic process carbohydrate derivative metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing carbohydrate derivative biosynthetic process glycosyl compound biosynthetic process wybutosine biosynthetic process tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process RNA modification biosynthetic process macromolecule modification metabolic process cellular process macromolecule metabolic process	-

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	IPR058240	Radical SAM superfamily	Homologous Superfamily
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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.