3CES | pdb_00003ces

Crystal Structure of E.coli MnmG (GidA), a Highly-Conserved tRNA Modifying Enzyme

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Thi4/GidA-like	8092224	3000051	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Helix-hairpin-helix tandem	8092228	3000163	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thi4/GidA-like	8092224	3000051	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Helix-hairpin-helix tandem	8092228	3000163	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Helix-hairpin-helix tandem	8092228	3000163	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thi4/GidA-like	8092224	3000051	SCOP2B (2022-06-29)
A	SCOP2 Family	GidA-like	8049416	4006485	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Thi4/GidA-like	8092224	3000051	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Helix-hairpin-helix tandem	8092228	3000163	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	GIDA_assoc_1st	e3cesD3	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)
D	GIDA	e3cesD5	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)
D	GIDA_assoc_1st,FAD_binding_3_1st	e3cesD4	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)
C	GIDA_assoc_1st	e3cesC3	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)
C	GIDA	e3cesC2	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)
C	FAD_binding_3_1st	e3cesC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: FAD_binding_3_1st	ECOD (1.6)
B	GIDA_assoc_1st	e3cesB2	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)
B	GIDA	e3cesB5	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)
B	GIDA_assoc_1st,FAD_binding_3_1st	e3cesB4	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)
A	GIDA_assoc_1st	e3cesA3	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	e3cesA2	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	e3cesA1	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)
D	2.40.30.260	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
C	2.40.30.260	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B	2.40.30.260	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
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, B, C, D	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, B, C, D	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, B, C, D	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 anion binding nucleotide binding heterocyclic compound binding small molecule binding	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 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 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 protein 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 regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process translation 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 cellular anatomical structure intracellular anatomical structure catalytic complex cytosolic tRNA wobble base thiouridylase complex sulfurtransferase complex transferase complex cytoplasm cytosol intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR004416	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG	Family
A, B, C, D	IPR020595	MnmG-related, conserved site	Conserved Site
A, B, C, D	IPR047001	tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal subdomain	Domain
A, B, C, D	IPR040131	MnmG, N-terminal domain	Domain
A, B, C, D	IPR049312	tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal, N-terninal subdomain	Domain
A, B, C, D	IPR026904	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG, C-terminal	Domain
A, B, C, D	IPR044920	tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal subdomain superfamily	Homologous Superfamily
A, B, C, D	IPR002218	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG-related	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 R01GM157729.