Annotations: 5CM2

Structure of Y. lipolytica Trm9-Trm112 complex, a methyltransferase modifying U34 in the anticodon loop of some tRNAs

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 [auth M]	KRIT1_FRMD8_FERM_C	e5cm2M1	A: a/b three-layered sandwiches	X: C-terminal additional helical subdomain in reovirus polymerase lambda3	H: C-terminal additional helical subdomain in reovirus polymerase lambda3	T: C-terminal additional helical subdomain in reovirus polymerase lambda3	F: KRIT1_FRMD8_FERM_C	ECOD (v294.1)
A [auth Z]	KRIT1_FRMD8_FERM_C	e5cm2Z1	A: a/b three-layered sandwiches	X: C-terminal additional helical subdomain in reovirus polymerase lambda3	H: C-terminal additional helical subdomain in reovirus polymerase lambda3	T: C-terminal additional helical subdomain in reovirus polymerase lambda3	F: KRIT1_FRMD8_FERM_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth M]	2.20.25.10	Mainly Beta	Single Sheet	N-terminal domain of TfIIb		CATH (4.3.0)
A [auth Z]	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
B [auth M]	PF03966	Trm112p-like protein (Trm112p)	Trm112p-like protein	The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. Trm112p is required for tRNA ...	The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. Trm112p is required for tRNA methylation in S. cerevisiae and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W [1]. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast [2]. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices [2].	Domain
A [auth Z]	PF08241	Methyltransferase domain (Methyltransf_11)	Methyltransferase domain	Members of this family are SAM dependent methyltransferases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth M]	TRNA METHYLTRANSFERASE ACTIVATOR SUBUNIT	tRNA methyltransferase activity RNA 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 tRNA (guanine(10)-N2)-methyltransferase activity N-methyltransferase activity methyltransferase activity catalytic activity rRNA methyltransferase activity tRNA methyltransferase activity RNA 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 tRNA (guanine(10)-N2)-methyltransferase activity N-methyltransferase activity methyltransferase activity catalytic activity rRNA methyltransferase activity catalytic activity, acting on a rRNA rRNA (guanine) methyltransferase activity enzyme regulator activity enzyme activator activity molecular function activator activity methyltransferase regulator activity molecular function regulator activity tRNA methyltransferase activator activity protein heterodimerization activity protein binding binding protein dimerization activity catalytic activity, acting on a protein protein methyltransferase activity cation binding ion binding metal ion binding small molecule binding	ribonucleoprotein complex biogenesis regulation of cellular process positive regulation of biological process RNA metabolic process rRNA processing positive regulation of rRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process positive regulation of metabolic process ribosome biogenesis nucleic acid biosynthetic process regulation of RNA metabolic process ribonucleoprotein complex biogenesis regulation of cellular process positive regulation of biological process RNA metabolic process rRNA processing positive regulation of rRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process positive regulation of metabolic process ribosome biogenesis nucleic acid biosynthetic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of rRNA processing macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process tRNA processing tRNA modification macromolecule methylation tRNA metabolic process RNA modification methylation macromolecule modification RNA methylation tRNA methylation tRNA wobble uridine modification tRNA wobble base modification ribosomal small subunit biogenesis maturation of SSU-rRNA RNA (guanine-N7)-methylation rRNA methylation rRNA modification rRNA (guanine-N7)-methylation rRNA base methylation ribosomal large subunit biogenesis maturation of LSU-rRNA	protein-containing complex tRNA (m2G10) methyltransferase complex intracellular anatomical structure cellular anatomical structure catalytic complex methyltransferase complex transferase complex tRNA methyltransferase complex cytoplasm eRF1 methyltransferase complex membrane-bounded organelle intracellular organelle organelle nucleus protein-containing complex tRNA (m2G10) methyltransferase complex intracellular anatomical structure cellular anatomical structure catalytic complex methyltransferase complex transferase complex tRNA methyltransferase complex cytoplasm eRF1 methyltransferase complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
A [auth Z]	TRNA METHYLTRANSFERASE	transferase activity, transferring one-carbon groups transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity tRNA (5-carboxymethyluridine(34)-5-O)-methyltransferase activity tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA tRNA (uridine) methyltransferase activity catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA RNA binding binding transferase activity, transferring one-carbon groups transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity tRNA (5-carboxymethyluridine(34)-5-O)-methyltransferase activity tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA tRNA (uridine) methyltransferase activity catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA RNA binding binding tRNA binding nucleic acid binding	RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process RNA modification biosynthetic process methylation macromolecule modification metabolic process cellular process macromolecule metabolic process RNA methylation tRNA methylation regulation of cellular process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of translational elongation protein metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process translation regulation of gene expression regulation of translation translational elongation regulation of macromolecule biosynthetic process regulation of metabolic process tRNA wobble uridine modification tRNA wobble base modification	protein-containing complex intracellular anatomical structure cellular anatomical structure catalytic complex methyltransferase complex transferase complex tRNA methyltransferase complex cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth M]	IPR039127	Multifunctional methyltransferase subunit Trm112	Family
B [auth M]	IPR005651	Trm112-like	Family
A [auth Z]	IPR051422	AlkB Family tRNA Methyltransferase/Dioxygenase	Family
A [auth Z]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A [auth Z]	IPR013216	Methyltransferase type 11	Domain

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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.