1UAM

Crystal structure of tRNA(m1G37)methyltransferase: Insight into tRNA recognition

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1uama1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	tRNA(m1G37)-methyltransferase TrmD	tRNA(m1G37)-methyltransferase TrmD	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
A	d1uama3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
A	d1uama2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	tRNA(m1G37)-methyltransferase TrmD	8022496	4000478	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	alpha/beta knot	8034876	3001122	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	PF01746	e1uamA1	A: a/b three-layered sandwiches	X: alpha/beta knot (From Topology)	H: alpha/beta knot (From Topology)	T: alpha/beta knot	F: PF01746	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
A	1.10.1270.20	Mainly Alpha	Orthogonal Bundle	Trp Operon Repressor	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01746	tRNA (Guanine-1)-methyltransferase (tRNA_m1G_MT)	tRNA (Guanine-1)-methyltransferase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	tRNA (Guanine-N(1)-)-methyltransferase	tRNA methyltransferase activity RNA methyltransferase activity tRNA (guanine(37)-N1)-methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid tRNA (guanine) methyltransferase activity catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent 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 N1-guanine 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	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR029026	tRNA (guanine-N1-)-methyltransferase, N-terminal	Homologous Superfamily
A	IPR029028	Alpha/beta knot methyltransferases	Homologous Superfamily
A	IPR016009	tRNA methyltransferase TRMD/TRM10-type domain	Domain
A	IPR023148	tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily	Homologous Superfamily
A	IPR002649	tRNA (guanine-N1-)-methyltransferase TrmD	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	tRNA-(m1-G37)-methyl transferase M-CSA #332	In transfer RNA many different modified nucleosides are found, especially in the anticodon region. tRNA (guanine (N1))-methyltransferase (TrmD) is one of several nucleases operating together with the tRNA-modifying enzymes before the formation of the mature tRNA. TrmD catalyses the S-adenosyl-methionine(AdoMet) dependent It methlyation of guanosine(G) to N1-methylguanine (1-methylguanosine (m1G)) at position 37 of tRNAs that read CUN (leucine), CCN(proline), and CGG (arginine) codons. The presence of m1G improves the cellular growth rate and the polypeptide steptime and also prevents the tRNA from shifting the reading frame.	Defined by 4 residues: PRO:A-109 [auth A-89]GLU:A-136 [auth A-116]ARG:A_2-174 [auth A_2-154]ASP:A_2-189 [auth A_2-169] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.1.1.31 (PDB Primary Data) Search M-CSA Motif + EC 2.1.1.31

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.