6ZXW

Structure of Archaeoglobus fulgidus Trm11-Trm112 m2G10 tRNA methyltransferase complex bound to sinefungin

External Resource: Annotation

Domain Annotation: ECOD Classification
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 H]	Trm112p	e6zxwH1	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Trm112p	ECOD (1.6)
A [auth G]	F_UNCLASSIFIED	e6zxwG1	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin-like domain in ThiI (From Topology)	T: Ferredoxin-like domain in ThiI	F: F_UNCLASSIFIED	ECOD (1.6)
A [auth G]	THUMP	e6zxwG2	A: a+b two layers	X: THUMP domain-like (From Topology)	H: THUMP domain-like (From Topology)	T: THUMP domain-like	F: THUMP	ECOD (1.6)
A [auth G]	UPF0020	e6zxwG3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: UPF0020	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth H]	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 G]	PF01170	RMKL-like, methyltransferase domain (UPF0020)	RMKL-like, methyltransferase domain	This domain is the methyltransferase domain found in ribosomal RNA large subunit methyltransferase K/L from Escherichia coli (RmlKL), tRNA (guanine(10)-N2)-dimethyltransferase from Methanocaldococcus jannaschii and similar proteins, which have a THU ...	This domain is the methyltransferase domain found in ribosomal RNA large subunit methyltransferase K/L from Escherichia coli (RmlKL), tRNA (guanine(10)-N2)-dimethyltransferase from Methanocaldococcus jannaschii and similar proteins, which have a THUMP domain at the N-terminal [1-4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth H]	Uncharacterized protein	cation binding ion binding binding metal ion binding small molecule binding	-	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol
A [auth G]	tRNA (Guanine(10)-N2)-dimethyltransferase	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 RNA binding 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 RNA binding binding organic cyclic compound binding tRNA binding nucleic acid binding tRNA (guanine(10)-N2)-dimethyltransferase activity	cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing cellular metabolic process tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing cellular metabolic process 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	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth H]	IPR005651	Trm112-like	Family
A [auth G]	IPR004114	THUMP domain	Domain
A [auth G]	IPR005885	tRNA guanine(10)-N2-dimethyltransferase	Family
A [auth G]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A [auth G]	IPR000241	Ribosomal RNA large subunit methyltransferase K/L-like, methyltransferase domain	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 R01GM133198.