4QTU

Structure of S. cerevisiae Bud23-Trm112 complex involved in formation of m7G1575 on 18S rRNA (SAM bound form)

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Trm112p	e4qtuA1	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Trm112p	ECOD (1.6)
C	Trm112p	e4qtuC1	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Trm112p	ECOD (1.6)
B	Methyltransf_11_1	e4qtuB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_1	ECOD (1.6)
D	Methyltransf_11_1	e4qtuD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.20.25.10	Mainly Beta	Single Sheet	N-terminal domain of TfIIb		CATH (4.3.0)
C	2.20.25.10	Mainly Beta	Single Sheet	N-terminal domain of TfIIb		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)
D	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, C	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
B, D	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
A, C	Multifunctional methyltransferase subunit TRM112	protein heterodimerization activity protein binding binding protein dimerization activity	cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis ribosomal large subunit biogenesis RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing tRNA modification primary metabolic process cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis ribosomal large subunit biogenesis 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 macromolecule metabolic process RNA methylation tRNA methylation regulation of cellular process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly regulation of biological process positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process regulation of gene expression regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of cellular component organization regulation of cellular component organization positive regulation of DNA-templated transcription positive regulation of biological process DNA-templated transcription termination positive regulation of termination of DNA-templated transcription cellular component organization positive regulation of biosynthetic process positive regulation of protein-containing complex disassembly positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process positive regulation of RNA biosynthetic process ribosomal small subunit biogenesis tRNA wobble uridine modification tRNA wobble base modification rRNA processing maturation of SSU-rRNA rRNA metabolic process RNA (guanine-N7)-methylation rRNA methylation rRNA modification rRNA (guanine-N7)-methylation rRNA base methylation maturation of LSU-rRNA	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm cytosol protein-containing complex tRNA (m2G10) methyltransferase complex catalytic complex methyltransferase complex transferase complex tRNA methyltransferase complex eRF1 methyltransferase complex ribosome
B, D	Putative methyltransferase BUD23	RNA methyltransferase activity rRNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity catalytic activity, acting on a rRNA S-adenosylmethionine-dependent methyltransferase activity methyltransferase activity catalytic activity rRNA (guanine) methyltransferase activity	establishment of organelle localization cellular localization ribonucleoprotein complex biogenesis nucleocytoplasmic transport transport nuclear transport ribosomal subunit export from nucleus intracellular transport establishment of localization protein-containing complex localization cellular component biogenesis localization ribosome biogenesis ribosomal small subunit export from nucleus organelle localization establishment of organelle localization cellular localization ribonucleoprotein complex biogenesis nucleocytoplasmic transport transport nuclear transport ribosomal subunit export from nucleus intracellular transport establishment of localization protein-containing complex localization cellular component biogenesis localization ribosome biogenesis ribosomal small subunit export from nucleus organelle localization establishment of localization in cell cellular process cellular component organization or biogenesis nuclear export ribosome localization RNA (guanine-N7)-methylation rRNA methylation RNA metabolic process rRNA processing nucleobase-containing compound metabolic process rRNA modification RNA biosynthetic process nucleic acid biosynthetic process RNA processing rRNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation RNA modification biosynthetic process methylation macromolecule modification rRNA (guanine-N7)-methylation metabolic process macromolecule metabolic process RNA methylation rRNA base methylation maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of SSU-rRNA endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of 5.8S rRNA ribosomal small subunit biogenesis maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen protein-containing complex catalytic complex methyltransferase complex transferase complex tRNA methyltransferase complex cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR039127	Multifunctional methyltransferase subunit Trm112	Family
A, C	IPR005651	Trm112-like	Family
B, D	IPR022238	18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23, C-terminal	Domain
B, D	IPR039769	18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23-like	Family
B, D	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
B, D	IPR013216	Methyltransferase type 11	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, D	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210

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.