1XZP | pdb_00001xzp

Structure of the GTP-binding protein TrmE from Thermotoga maritima

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)
B	d1xzpb1	Alpha and beta proteins (a+b)	Folate-binding domain	Folate-binding domain	TrmE formyl-THF-binding domain	TrmE formyl-THF-binding domain	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d1xzpb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d1xzpa1	All alpha proteins	Four-helical up-and-down bundle	TrmE connector domain	TrmE connector domain	TrmE connector domain	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d1xzpa2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	TrmE GTPase domain	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d1xzpa3	Alpha and beta proteins (a+b)	Folate-binding domain	Folate-binding domain	TrmE formyl-THF-binding domain	TrmE formyl-THF-binding domain	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d1xzpa4	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Folate-binding domain-like	8002420	3000025	SCOP2B (2022-06-29)
A	SCOP2 Family	TrmE formyl-THF-binding domain-like	8002419	4000140	SCOP2 (2022-06-29)
A	SCOP2 Family	50S ribosome-binding GTPase-like	8002424	4004038	SCOP2 (2022-06-29)
A	SCOP2 Family	TrmE connector domain-like	8056827	4000307	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Folate-binding domain-like	8002420	3000025	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ras-like P-loop GTPases	8002425	3002022	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	TrmE connector domain-like	8056828	3000076	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	GATase_2	e1xzpB1	A: alpha bundles	X: EGF-like	H: General secretion pathway protein M (EpsM) periplasmic domain-related	T: General secretion pathway protein M (EpsM) periplasmic domain-related	F: GATase_2	ECOD (develop294)
A	MnmE_helical	e1xzpA1	A: alpha bundles	X: Four-helical up-and-down bundle	H: TrmE connector domain	T: TrmE connector domain	F: MnmE_helical	ECOD (develop294)
A	TrmE_N	e1xzpA2	A: a+b two layers	X: Alpha-beta plaits	H: Aminomethyltransferase folate-binding domain	T: Aminomethyltransferase folate-binding domain	F: TrmE_N	ECOD (develop294)
A	Vps4_C,AAA_lid_3	e1xzpA6	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: Vps4_C,AAA_lid_3	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.1360.120	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
A	3.30.1360.120	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
A	1.20.120.430	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	tRNA modification GTPase MnmE domain 2	CATH (4.3.0)
A	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
B	PF10396	GTP-binding protein TrmE N-terminus (TrmE_N)	GTP-binding protein TrmE N-terminus	-	Family
A	PF12631	MnmE helical domain (MnmE_helical)	MnmE helical domain	-	Family
A	PF10396	GTP-binding protein TrmE N-terminus (TrmE_N)	GTP-binding protein TrmE N-terminus	-	Family
A	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
B	Probable tRNA modification GTPase trmE	binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding metal ion binding 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 identical protein binding protein 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
A	Probable tRNA modification GTPase trmE	binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding metal ion binding 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 identical protein binding protein 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
B	IPR005225	Small GTP-binding domain	Domain
B	IPR027266	Aminomethyltransferase superfamily	Homologous Superfamily
B	IPR018948	GTP-binding protein TrmE, N-terminal	Domain
B	IPR031168	TrmE-type guanine nucleotide-binding domain	Domain
B	IPR004520	tRNA modification GTPase MnmE	Family
B	IPR027368	tRNA modification GTPase MnmE domain 2	Homologous Superfamily
B	IPR008144	Guanylate kinase-like domain	Domain
B	IPR006073	GTP binding domain	Domain
B	IPR025867	MnmE, helical domain	Domain
B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR005225	Small GTP-binding domain	Domain
A	IPR027266	Aminomethyltransferase superfamily	Homologous Superfamily
A	IPR018948	GTP-binding protein TrmE, N-terminal	Domain
A	IPR031168	TrmE-type guanine nucleotide-binding domain	Domain
A	IPR004520	tRNA modification GTPase MnmE	Family
A	IPR027368	tRNA modification GTPase MnmE domain 2	Homologous Superfamily
A	IPR008144	Guanylate kinase-like domain	Domain
A	IPR006073	GTP binding domain	Domain
A	IPR025867	MnmE, helical domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily