Annotations: 3CP2

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Helix-hairpin-helix tandem	8092228	3000163	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thi4/GidA-like	8092224	3000051	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	GIDA_assoc_1st	e3cp2A3	A: alpha arrays	X: C-terminal helical domain in tRNA modifying enzyme GidA (From Topology)	H: C-terminal helical domain in tRNA modifying enzyme GidA (From Topology)	T: C-terminal helical domain in tRNA modifying enzyme GidA	F: GIDA_assoc_1st	ECOD (1.6)
A	GIDA	e3cp2A2	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C (From Topology)	T: FAD-linked reductases-C	F: GIDA	ECOD (1.6)
A	GIDA_assoc_1st,FAD_binding_3_1st	e3cp2A1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: GIDA_assoc_1st,FAD_binding_3_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.30.260	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
A	1.10.10.1800	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG/GidA	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21680	tRNA modifying enzyme MnmG/GidA C-terminal helical domain (GIDA_C_1st)	tRNA modifying enzyme MnmG/GidA C-terminal helical domain	The GidA associated domain is a domain that has been identified at the C-terminus of protein GidA. It consists of several helices, the last three being rather short and forming small bundle. GidA is an tRNA modification enzyme found in bacteria and m ...	The GidA associated domain is a domain that has been identified at the C-terminus of protein GidA. It consists of several helices, the last three being rather short and forming small bundle. GidA is an tRNA modification enzyme found in bacteria and mitochondrial. Based on mutational analysis this domain has been suggested to be implicated in binding of the D-stem of tRNA [2] and, in particular the small bundle, to be responsible for the interaction with protein MnmE [1]. Structures of GidA in complex with either tRNA or MnmE are missing. Reported to bind to Pfam family MnmE, Pfam:PF12631. This entry represents the first helices of the GidA associated domain. The last three helices are covered in Pfam:PF13932.	Domain
A	PF01134	Glucose inhibited division protein A (GIDA)	Glucose inhibited division protein A	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity flavin adenine dinucleotide binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding	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 ncRNA metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA methylation tRNA methylation tRNA wobble uridine modification tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation tRNA wobble base modification response to light stimulus response to stimulus response to radiation response to abiotic stimulus response to UV regulation of cytoplasmic translational fidelity regulation of cellular process organonitrogen compound biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of translational elongation regulation of biological quality protein metabolic process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process regulation of protein metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process translation regulation of cellular biosynthetic process regulation of cytoplasmic translational elongation regulation of gene expression regulation of translation translational elongation cytoplasmic translation regulation of macromolecule biosynthetic process cytoplasmic translational elongation regulation of translational fidelity regulation of metabolic process	protein-containing complex intracellular anatomical structure catalytic complex cytosolic tRNA wobble base thiouridylase complex cytoplasm cellular anatomical entity cytosol intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR004416	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG	Family
A	IPR020595	MnmG-related, conserved site	Conserved Site
A	IPR047001	tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal subdomain	Domain
A	IPR040131	MnmG, N-terminal domain	Domain
A	IPR049312	tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal, N-terninal subdomain	Domain
A	IPR026904	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG, C-terminal	Domain
A	IPR044920	tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal subdomain superfamily	Homologous Superfamily
A	IPR002218	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG-related	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.