3LHD

Crystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with S-adenosyl-L-homocysteine

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth A]	d3lhda_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Pyrococcus abyssi GE5 ) [TaxId: 272844 ],	SCOPe (2.08)
C [auth B]	d3lhdb_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Pyrococcus abyssi GE5 ) [TaxId: 272844 ],	SCOPe (2.08)
D	d3lhdd_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Pyrococcus abyssi GE5 ) [TaxId: 272844 ],	SCOPe (2.08)
A [auth C]	d3lhdc_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Pyrococcus abyssi GE5 ) [TaxId: 272844 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth A]	SCOP2B Superfamily	Transcription elongation factor GreA/GreB-like	8090667	3002449	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8083869	3000118	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8083869	3000118	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Transcription elongation factor GreA/GreB-like	8090667	3002449	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8083869	3000118	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Transcription elongation factor GreA/GreB-like	8090667	3002449	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	Transcription elongation factor GreA/GreB-like	8090667	3002449	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8083869	3000118	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 [auth A]	GCD14_N	e3lhdA1	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: GCD14_N	ECOD (1.6)
B [auth A]	Methyltransf_11_4	e3lhdA2	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)
C [auth B]	GCD14_N	e3lhdB1	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: GCD14_N	ECOD (1.6)
C [auth B]	Methyltransf_11_4	e3lhdB2	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)
D	GCD14_N	e3lhdD1	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: GCD14_N	ECOD (1.6)
D	Methyltransf_11_4	e3lhdD2	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 [auth C]	GCD14_N	e3lhdC1	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: GCD14_N	ECOD (1.6)
A [auth C]	Methyltransf_11_4	e3lhdC2	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 [auth A]	3.10.330.20	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	CATH (4.3.0)
B [auth A]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
C [auth B]	3.10.330.20	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	CATH (4.3.0)
C [auth B]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
D	3.10.330.20	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	CATH (4.3.0)
D	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
A [auth C]	3.10.330.20	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	CATH (4.3.0)
A [auth C]	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 [auth C], B [auth A], C [auth B], D	PF14801	tRNA methyltransferase complex GCD14 subunit N-term (GCD14_N)	tRNA methyltransferase complex GCD14 subunit N-term	This is the N-terminal domain of GCD14, itself a subunit of the tRNA methyltransferase complex that is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA [1]. The exact function of the N-terminus is not known but i ...	This is the N-terminal domain of GCD14, itself a subunit of the tRNA methyltransferase complex that is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA [1]. The exact function of the N-terminus is not known but it is necessary for maintaining the overall folding and for full enzymatic activity.	Domain
A [auth C], B [auth A], C [auth B], D	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 [auth C], B [auth A], C [auth B], D	SAM-dependent methyltransferase, putative	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 tRNA (adenine(57)-N1)/(adenine(58)-N1)-methyltransferase 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 ncRNA metabolic process 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

InterPro: Protein Family Classification InterPro Database Homepage

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.