2ZW9 | pdb_00002zw9

Crystal structure of tRNA wybutosine synthesizing enzyme TYW4

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	YonK	e2zw9B2	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: YonK	ECOD (v294.1)
B	PI3K_rbd,PIK3CG_ABD	e2zw9B3	A: a/b three-layered sandwiches	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (v294.1)
A	YonK	e2zw9A1	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: YonK	ECOD (v294.1)
A	PI3K_rbd,PIK3CG_ABD	e2zw9A2	A: a/b three-layered sandwiches	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
B	2.120.10.80	Mainly Beta	6 Propeller	Neuraminidase	Kelch-type beta propeller	CATH (4.3.0)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
A	2.120.10.80	Mainly Beta	6 Propeller	Neuraminidase	Kelch-type beta propeller	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01344	Kelch motif (Kelch_1)	Kelch motif	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Leucine carboxyl methyltransferase 2	tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity methyltransferase activity 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 metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification tRNA modification 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 RNA modification biosynthetic process tRNA processing macromolecule modification metabolic process cellular process macromolecule metabolic process RNA processing carbohydrate derivative metabolic process carbohydrate derivative biosynthetic process glycosyl compound biosynthetic process wybutosine biosynthetic process macromolecule methylation methylation RNA methylation tRNA methylation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR007213	Methyltransferase Ppm1/Ppm2/Tcmp	Family
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B	IPR006652	Kelch repeat type 1	Repeat
A, B	IPR011043	Galactose oxidase/kelch, beta-propeller	Homologous Superfamily
A, B	IPR015915	Kelch-type beta-propeller	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.