8DPB | pdb_00008dpb

MeaB in complex with the cobalamin-binding domain of its target mutase with GMPPCP bound

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	Simibi-like P-loop NTPases	8058232	3002018	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Simibi-like P-loop NTPases	8058232	3002018	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	ArgK	e8dpbA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ArgK	ECOD (1.6)
B	ArgK	e8dpbB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ArgK	ECOD (1.6)
C	B12-binding	e8dpbC1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)
D	B12-binding	e8dpbD1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03308	Methylmalonyl Co-A mutase-associated GTPase MeaB (MeaB)	Methylmalonyl Co-A mutase-associated GTPase MeaB	Family members were previously thought to be ArgK proteins acting as ATPase enzymes and kinases. They are now believed to be methylmalonyl Co-A mutase-associated GTPase MeaB. Structural studies of MeaB and the human ortholog (methylmalonyl associated ...	Family members were previously thought to be ArgK proteins acting as ATPase enzymes and kinases. They are now believed to be methylmalonyl Co-A mutase-associated GTPase MeaB. Structural studies of MeaB and the human ortholog (methylmalonyl associated protein A) MMAA, reveal alpha-helical domains at the N- and C-termini as well as a Ras-like GTPase domain. Mutational analysis of MeaB, show prohibited growth in Methylobacterium due to the inability to convert methylmalonyl-CoA to succinyl-CoA caused by an inactive form of methylmalonyl-CoA mutatase (mcm). In humans, mutations in (MMAA) are associated with the fatal disease methylmalonyl aciduria [1].	Domain
C, D	PF02310	B12 binding domain (B12-binding)	B12 binding domain	This domain binds to B12 (adenosylcobamide)[1-3], it is found in several enzymes, such as glutamate mutase Swiss:Q05488, methionine synthase Swiss:Q99707 and methylmalonyl-CoA mutase Swiss:P22033. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, ...	This domain binds to B12 (adenosylcobamide)[1-3], it is found in several enzymes, such as glutamate mutase Swiss:Q05488, methionine synthase Swiss:Q99707 and methylmalonyl-CoA mutase Swiss:P22033. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, which is important for B12 binding [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Methylmalonyl-CoA mutase accessory protein	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	-	cellular anatomical structure intracellular anatomical structure cytoplasm
C, D	Methylmalonyl-CoA mutase, alpha subunit	vitamin binding binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding methylmalonyl-CoA mutase activity isomerase activity catalytic activity intramolecular transferase activity cation binding ion binding metal ion binding	fatty acid metabolic process oxoacid metabolic process short-chain fatty acid metabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process propionate metabolic process, methylmalonyl pathway metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process propionate metabolic process lipid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR005129	SIMIBI class G3E GTPase, ArgK/MeaB	Family
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C, D	IPR006099	Methylmalonyl-CoA mutase, alpha/beta chain, catalytic	Domain
C, D	IPR036724	Cobalamin-binding domain superfamily	Homologous Superfamily
C, D	IPR006098	Methylmalonyl-CoA mutase, alpha chain, catalytic	Domain
C, D	IPR006159	Methylmalonyl-CoA mutase, C-terminal	Domain
C, D	IPR006158	Cobalamin (vitamin B12)-binding domain	Domain
C, D	IPR016176	Cobalamin (vitamin B12)-dependent enzyme, catalytic	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.