2PWY | pdb_00002pwy

Crystal Structure of a m1A58 tRNA methyltransferase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2pwyb_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Thermus thermophilus HB27 ) [TaxId: 262724 ],	SCOPe (2.08)
A	d2pwya_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Thermus thermophilus HB27 ) [TaxId: 262724 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Transcription elongation factor, GreA/GreB-like	8090668	3002449	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8083871	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8083871	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Transcription elongation factor, GreA/GreB-like	8090668	3002449	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	GCD14_N	e2pwyB1	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: GCD14_N	ECOD (1.6)
B	Methyltransf_11_4	e2pwyB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_4	ECOD (1.6)
A	GCD14_N	e2pwyA2	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: GCD14_N	ECOD (1.6)
A	Methyltransf_11_4	e2pwyA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_4	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)
A	3.10.330.20	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	tRNA (adenine-N(1)-)-methyltransferase	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	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 tRNA modification macromolecule methylation RNA modification methylation macromolecule modification RNA methylation tRNA methylation	protein-containing complex tRNA (m1A) methyltransferase complex intracellular anatomical structure cellular anatomical structure catalytic complex methyltransferase complex transferase complex tRNA methyltransferase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR014816	tRNA (1-methyladenosine) methyltransferase catalytic subunit Gcd14	Family
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.