Annotations: 3TMA

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF21888	e3tmaA3	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin-like domain in ThiI (From Topology)	T: Ferredoxin-like domain in ThiI	F: PF21888	ECOD (1.6)
A	PF02926	e3tmaA2	A: a+b two layers	X: THUMP domain-like (From Topology)	H: THUMP domain-like (From Topology)	T: THUMP domain-like	F: PF02926	ECOD (1.6)
A	PF01170	e3tmaA4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF01170	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.2130.30	Alpha Beta	2-Layer Sandwich	VC0802-like		CATH (4.2.0)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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
A	PF21888	Ferredoxin-like NFLD domain (NFLD)	Ferredoxin-like NFLD domain	This entry represents the NFLD domain, a domain found fused to the N-terminus of certain RNA methyltransferases (MTases), particularly in the TrmN/Trm14 family. The NFLD domain, which consists of a beta-sheet and two alpha-helices, was initially prop ...	This entry represents the NFLD domain, a domain found fused to the N-terminus of certain RNA methyltransferases (MTases), particularly in the TrmN/Trm14 family. The NFLD domain, which consists of a beta-sheet and two alpha-helices, was initially proposed to be an ancient RNA binding domain based on bioinformatics analyses. The NFLD domain is often fused to the minimal core of the THUMP domain, and together, they contribute to tRNA recognition and catalysis.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	methyltransferase	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(6)-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(6)-N2)-methyltransferase activity N-methyltransferase activity methyltransferase activity catalytic activity RNA binding binding organic cyclic compound binding nucleic acid binding	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
A	IPR004114	THUMP domain	Domain
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	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.