6DJT | pdb_00006djt

Structure of TYW1 with a lysine-pyruvate adduct bound

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	FAD_binding_3	e6djtA1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: FAD_binding_3	ECOD (v294.1)

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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF04055	Radical SAM superfamily (Radical_SAM)	Radical SAM superfamily	Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.	Domain
A	PF08608	Wyosine base formation (Wyosine_form)	Wyosine base formation	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase	iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion 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 iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion 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	RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing metabolic process cellular process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing metabolic process cellular process macromolecule metabolic process RNA processing	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR007197	Radical SAM	Domain
A	IPR058240	Radical SAM superfamily	Homologous Superfamily
A	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A	IPR013917	tRNA wybutosine-synthesis	Domain
A	IPR023993	S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase, archaea	Family
A	IPR034556	S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	KPI	Parent Component: LYS RESID: AA0287 PSI-MOD : N6-pyruvic acid 2-iminyl-L-lysine MOD:00292

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.