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)
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]	F_UNCLASSIFIED	e6zxwG2	A: a+b two layers	X: THUMP domain-like (From Topology)	H: THUMP domain-like (From Topology)	T: THUMP domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
A [auth G]	PF01170	e6zxwG3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF01170	ECOD (1.6)
B [auth H]	PF03966	e6zxwH1	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: PF03966	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
A [auth G]	PF02926	THUMP domain (THUMP)	THUMP domain	The THUMP domain is named after after thiouridine synthases, methylases and PSUSs [1]. The THUMP domain consists of about 110 amino acid residues. This domain is found in many tRNA modification enzymes classified into five types, namely 4-thiouridine ...	The THUMP domain is named after after thiouridine synthases, methylases and PSUSs [1]. The THUMP domain consists of about 110 amino acid residues. This domain is found in many tRNA modification enzymes classified into five types, namely 4-thiouridine synthetase, deaminase, methyltransferase, a partner protein of acetyltransferase and pseudouridine synthase [3]. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterised RNA-binding domains [2-3] and was first predicted to function by delivering a variety of RNA modification enzymes to their targets [1]. Studies performed in tRNA 4-thiouridine synthetase, tRNA methyltransferases and tRNA deaminase suggest that the THUMP domain captures the 3'-end of RNA but in some cases this is not applicable due to the modification patterns observed in tRNA [3]. Several THUMP-related proteins are also involved in other RNAs modifications, such as rRNA modification [3].	Domain
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 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 nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA methylation tRNA methylation	intracellular anatomical structure cytoplasm cellular anatomical entity
B [auth H]	Uncharacterized protein	cation binding ion binding binding metal ion binding small molecule binding	-	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
B [auth H]	IPR005651	Trm112-like	Family

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.