2GJ8

Structure of the MnmE G-domain in complex with GDP*AlF4-, Mg2+ and K+

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2gj8a_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
B	d2gj8b_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
C	d2gj8c_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
D	d2gj8d2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
D	d2gj8d3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	50S ribosome-binding GTPase-like	8019249	4004038	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ras-like P-loop GTPases	8058049	3002022	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8058049	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8058049	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8058049	3002022	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	MnmE_helical_2nd	e2gj8A1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MnmE_helical_2nd	ECOD (1.6)
B	MnmE_helical_2nd	e2gj8B1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MnmE_helical_2nd	ECOD (1.6)
C	MnmE_helical_2nd	e2gj8C1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MnmE_helical_2nd	ECOD (1.6)
D	MnmE_helical_2nd	e2gj8D1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MnmE_helical_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF12631	MnmE helical domain (MnmE_helical)	MnmE helical domain	-	Family
A, B, C, D	PF01926	50S ribosome-binding GTPase (MMR_HSR1)	50S ribosome-binding GTPase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	tRNA modification GTPase trmE	cation binding ion binding binding potassium ion binding alkali metal ion binding metal ion binding small molecule binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding cation binding ion binding binding potassium ion binding alkali metal ion binding metal ion binding small molecule binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding GDP binding identical protein binding protein binding protein homodimerization activity protein dimerization activity pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	primary metabolic process gene expression chaperone-mediated protein folding macromolecule biosynthetic process protein maturation protein folding biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process response to stimulus response to pH response to abiotic stimulus primary metabolic process gene expression chaperone-mediated protein folding macromolecule biosynthetic process protein maturation protein folding biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process response to stimulus response to pH response to abiotic stimulus RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing tRNA modification nucleobase-containing compound biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process RNA modification methylation macromolecule modification RNA methylation tRNA methylation tRNA wobble uridine modification tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation tRNA wobble base modification regulation of cytoplasmic translational fidelity regulation of cellular process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of translational elongation regulation of biological quality 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 cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR018948	GTP-binding protein TrmE, N-terminal	Domain
A, B, C, D	IPR031168	TrmE-type guanine nucleotide-binding domain	Domain
A, B, C, D	IPR004520	tRNA modification GTPase MnmE	Family
A, B, C, D	IPR025867	MnmE, helical domain	Domain
A, B, C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D	IPR005225	Small GTP-binding domain	Domain
A, B, C, D	IPR027368	tRNA modification GTPase MnmE domain 2	Homologous Superfamily
A, B, C, D	IPR006073	GTP binding domain	Domain
A, B, C, D	IPR027266	GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1	Homologous Superfamily

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.