2ZXI | pdb_00002zxi

Structure of Aquifex aeolicus GidA in the form II crystal

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)
B	SCOP2B Superfamily	Thi4/GidA-like	8092223	3000051	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Helix-hairpin-helix tandem	8092227	3000163	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Helix-hairpin-helix tandem	8092227	3000163	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thi4/GidA-like	8092223	3000051	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Helix-hairpin-helix tandem	8092227	3000163	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thi4/GidA-like	8092223	3000051	SCOP2B (2022-06-29)
A	SCOP2 Family	GidA-like	8049415	4006485	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Thi4/GidA-like	8092223	3000051	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Helix-hairpin-helix tandem	8092227	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)
B	YonK	e2zxiB1	A: alpha bundles	X: DP domain	H: DP domain	T: DP domain	F: YonK	ECOD (develop294)
D	DcpS_C	e2zxiD8	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: DcpS_C	ECOD (develop294)
C	GIDA	e2zxiC7	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: GIDA	ECOD (develop294)
C	S-AdoMet_synt_N	e2zxiC10	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: S-AdoMet_synt_N	ECOD (develop294)
C	FAD_binding_2, GIDA	e2zxiC2	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: FAD_binding_2, GIDA	ECOD (develop294)
A	GIDA_C_1st	e2zxiA1	A: alpha bundles	X: Single-stranded left-handed beta-helix	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: GIDA_C_1st	ECOD (develop294)
A	GIDA_C	e2zxiA4	A: alpha bundles	X: Single-stranded left-handed beta-helix	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: GIDA_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.40.30.260	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B	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)
B	1.10.150.570	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
D	2.40.30.260	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
D	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)
D	1.10.150.570	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
C	2.40.30.260	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
C	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)
C	1.10.150.570	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	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)
A	1.10.150.570	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF13932	tRNA modifying enzyme MnmG/GidA C-terminal helical bundle (SAM_GIDA_C)	tRNA modifying enzyme MnmG/GidA C-terminal helical bundle	The GidA associated domain is a domain that has been identified at the C-terminus of protein GidA. It consists of several helices, last three being rather short and forming small bundle and are represented in this entry. GidA is a tRNA modification e ...	The GidA associated domain is a domain that has been identified at the C-terminus of protein GidA. It consists of several helices, last three being rather short and forming small bundle and are represented in this entry. GidA is a tRNA modification enzyme found in bacteria and mitochondrial. Based on mutational analysis the C-terminal helices have been suggested to be implicated in binding of the D-stem of tRNA [2] and, specifically this domain, 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.	Domain
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 mnmG	flavin adenine dinucleotide binding 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 modification	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.