5EQJ

Crystal structure of the two-subunit tRNA m1A58 methyltransferase from Saccharomyces cerevisiae

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	tRNA (1-methyladenosine)-methyltransferase non-catalytic subunit TRM6-like	8045535	4004521	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090620	3000118	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Transcription elongation factor GreA/GreB-like	8090671	3002449	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	PF04189	e5eqjA2	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: PF04189	ECOD (1.6)
A	PF04189	e5eqjA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF04189	ECOD (1.6)
B	F_UNCLASSIFIED	e5eqjB1	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF08704	e5eqjB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF08704	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.10.330.20	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	CATH (4.3.0)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF04189	Gcd10p family (Gcd10p)	Gcd10p family	-	Family
B	PF08704	tRNA methyltransferase complex GCD14 subunit (GCD14)	tRNA methyltransferase complex GCD14 subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6	RNA binding binding organic cyclic compound binding nucleic acid binding	cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing cellular metabolic process tRNA modification primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing cellular metabolic process tRNA modification primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process organic cyclic compound metabolic process RNA modification biosynthetic process methylation macromolecule modification nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA methylation tRNA methylation	protein-containing complex tRNA (m1A) methyltransferase complex intracellular anatomical structure catalytic complex methyltransferase complex transferase complex cellular anatomical entity tRNA methyltransferase complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
B	tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRM61	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 S-adenosylmethionine-dependent methyltransferase activity tRNA (adenine) methyltransferase activity tRNA (adenine(58)-N1)-methyltransferase activity methyltransferase activity catalytic activity	cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing cellular metabolic process tRNA modification primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing cellular metabolic process tRNA modification primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process organic cyclic compound metabolic process RNA modification biosynthetic process methylation macromolecule modification nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA methylation tRNA methylation	protein-containing complex tRNA (m1A) methyltransferase complex intracellular anatomical structure catalytic complex methyltransferase complex transferase complex cellular anatomical entity tRNA methyltransferase complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR017423	tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6	Family
B	IPR014816	tRNA (1-methyladenosine) methyltransferase catalytic subunit Gcd14	Family
B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
B	IPR049470	tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRM61, C-terminal	Domain

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.