3GEI | pdb_00003gei

Crystal structure of MnmE from Chlorobium tepidum in complex with GCP

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)
A	SCOP2B Superfamily	Folate-binding domain-like	8056836	3000025	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TrmE connector domain-like	8056840	3000076	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TrmE connector domain-like	8056840	3000076	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TrmE connector domain-like	8056840	3000076	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Folate-binding domain-like	8056836	3000025	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TrmE connector domain-like	8056840	3000076	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TrmE connector domain-like	8056840	3000076	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TrmE connector domain-like	8056840	3000076	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Folate-binding domain-like	8056836	3000025	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	ABC_tran	e3geiA7	A: a/b three-layered sandwiches	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: ABC_tran	ECOD (v294.1)
B	ClpB_D2-small	e3geiB13	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ClpB_D2-small	ECOD (v294.1)
C	PDEase_I	e3geiC1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
B	3.30.1360.120	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
B	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)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.30.1360.120	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
C	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF12631	MnmE helical domain (MnmE_helical)	MnmE helical domain	-	Family
A, B, C	PF10396	GTP-binding protein TrmE N-terminus (TrmE_N)	GTP-binding protein TrmE N-terminus	-	Family
A, B, C	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	tRNA modification GTPase mnmE	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
A, B, C	IPR005225	Small GTP-binding domain	Domain
A, B, C	IPR027266	Aminomethyltransferase superfamily	Homologous Superfamily
A, B, C	IPR018948	GTP-binding protein TrmE, N-terminal	Domain
A, B, C	IPR031168	TrmE-type guanine nucleotide-binding domain	Domain
A, B, C	IPR004520	tRNA modification GTPase MnmE	Family
A, B, C	IPR027368	tRNA modification GTPase MnmE domain 2	Homologous Superfamily
A, B, C	IPR006073	GTP binding domain	Domain
A, B, C	IPR025867	MnmE, helical domain	Domain
A, B, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.