5MVI | pdb_00005mvi

Crystal structure of 2-methylcitrate dehydratase (PrpD) from Salmonella enterica

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
C [auth A]	d5mvia_	Multi-domain proteins (alpha and beta)	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	automated matches	(Salmonella enterica ) [TaxId: 28901 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth E]	MmgE_PrpD_1st	e5mviE1	A: alpha arrays	X: alpha-helical domain in 2-methylcitrate dehydratase PrpD (From Topology)	H: alpha-helical domain in 2-methylcitrate dehydratase PrpD (From Topology)	T: alpha-helical domain in 2-methylcitrate dehydratase PrpD	F: MmgE_PrpD_1st	ECOD (1.6)
B [auth D]	MmgE_PrpD_1st	e5mviD1	A: alpha arrays	X: alpha-helical domain in 2-methylcitrate dehydratase PrpD (From Topology)	H: alpha-helical domain in 2-methylcitrate dehydratase PrpD (From Topology)	T: alpha-helical domain in 2-methylcitrate dehydratase PrpD	F: MmgE_PrpD_1st	ECOD (1.6)
C [auth A]	MmgE_PrpD_1st	e5mviA1	A: alpha arrays	X: alpha-helical domain in 2-methylcitrate dehydratase PrpD (From Topology)	H: alpha-helical domain in 2-methylcitrate dehydratase PrpD (From Topology)	T: alpha-helical domain in 2-methylcitrate dehydratase PrpD	F: MmgE_PrpD_1st	ECOD (1.6)
C [auth A]	MmgE_PrpD_2nd	e5mviA2	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Serine dehydratase beta chain-like (From Topology)	T: Serine dehydratase beta chain-like	F: MmgE_PrpD_2nd	ECOD (1.6)
D [auth B]	MmgE_PrpD_1st	e5mviB1	A: alpha arrays	X: alpha-helical domain in 2-methylcitrate dehydratase PrpD (From Topology)	H: alpha-helical domain in 2-methylcitrate dehydratase PrpD (From Topology)	T: alpha-helical domain in 2-methylcitrate dehydratase PrpD	F: MmgE_PrpD_1st	ECOD (1.6)
E [auth C]	MmgE_PrpD_1st	e5mviC1	A: alpha arrays	X: alpha-helical domain in 2-methylcitrate dehydratase PrpD (From Topology)	H: alpha-helical domain in 2-methylcitrate dehydratase PrpD (From Topology)	T: alpha-helical domain in 2-methylcitrate dehydratase PrpD	F: MmgE_PrpD_1st	ECOD (1.6)
F	MmgE_PrpD_1st	e5mviF1	A: alpha arrays	X: alpha-helical domain in 2-methylcitrate dehydratase PrpD (From Topology)	H: alpha-helical domain in 2-methylcitrate dehydratase PrpD (From Topology)	T: alpha-helical domain in 2-methylcitrate dehydratase PrpD	F: MmgE_PrpD_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth E]	1.10.4100.10	Mainly Alpha	Orthogonal Bundle	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	CATH (utative)
B [auth D]	1.10.4100.10	Mainly Alpha	Orthogonal Bundle	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	CATH (utative)
C [auth A]	1.10.4100.10	Mainly Alpha	Orthogonal Bundle	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	CATH (4.3.0)
C [auth A]	3.30.1330.120	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
D [auth B]	1.10.4100.10	Mainly Alpha	Orthogonal Bundle	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	CATH (utative)
E [auth C]	1.10.4100.10	Mainly Alpha	Orthogonal Bundle	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	CATH (utative)
F	1.10.4100.10	Mainly Alpha	Orthogonal Bundle	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], F	PF19305	MmgE/PrpD C-terminal domain (MmgE_PrpD_C)	MmgE/PrpD C-terminal domain	This entry represents the C-terminal domain of 2-methylcitrate dehydratase EC:4.2.1.79 (PrpD) that is required for propionate catabolism. It catalyses the third step of the 2-methylcitric acid cycle. This domain is related to the serine dehydratase b ...	This entry represents the C-terminal domain of 2-methylcitrate dehydratase EC:4.2.1.79 (PrpD) that is required for propionate catabolism. It catalyses the third step of the 2-methylcitric acid cycle. This domain is related to the serine dehydratase beta chain.	Domain
A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], F	PF03972	MmgE/PrpD N-terminal domain (MmgE_PrpD_N)	MmgE/PrpD N-terminal domain	This entry represents the N-terminal domain of 2-methylcitrate dehydratase EC:4.2.1.79 (PrpD) that is required for propionate catabolism. It catalyses the third step of the 2-methylcitric acid cycle [1]. This enzyme consists of two domains: a large d ...	This entry represents the N-terminal domain of 2-methylcitrate dehydratase EC:4.2.1.79 (PrpD) that is required for propionate catabolism. It catalyses the third step of the 2-methylcitric acid cycle [1]. This enzyme consists of two domains: a large domain with an all-helical fold and a smaller domain that folds into an alpha/beta domain [2]. Cis-aconitic acid decarboxylase (CAD) shares high identity with proteins of the MmgE/PrpD family [3,4]. Citrate/2-methylcitrate dehydratase from Bacillus subtilis is involved in the tricarboxylic acid (TCA) and methylcitric acid cycles as it has both 2-methylcitrate dehydratase and citrate dehydratase activities [5]. This entry represents the N-terminal domain of 2-methylcitrate dehydratase PrpD, which has an all-helical fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], F	2-methylcitrate dehydratase	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding aconitate hydratase activity hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity 2-methylcitrate dehydratase activity	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy fatty acid metabolic process oxoacid metabolic process short-chain fatty acid metabolic process carboxylic acid metabolic process organic acid metabolic process small molecule metabolic process aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy fatty acid metabolic process oxoacid metabolic process short-chain fatty acid metabolic process carboxylic acid metabolic process organic acid metabolic process small molecule metabolic process propionate metabolic process, methylcitrate cycle monocarboxylic acid metabolic process propionate metabolic process lipid metabolic process short-chain fatty acid catabolic process lipid catabolic process catabolic process organic acid catabolic process fatty acid catabolic process propionate catabolic process propionate catabolic process, 2-methylcitrate cycle monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], F	IPR036148	MmgE/PrpD superfamily	Homologous Superfamily
A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], F	IPR012705	2-methylcitrate dehydratase PrpD	Family
A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], F	IPR005656	MmgE/PrpD	Family
A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], F	IPR042188	MmgE/PrpD superfamily, domain 2	Homologous Superfamily
A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], F	IPR042183	MmgE/PrpD superfamily, domain 1	Homologous Superfamily
A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], F	IPR045337	MmgE/PrpD, C-terminal	Domain
A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], A [auth E], B [auth D], C [auth A], D [auth B], E [auth C], F	IPR045336	MmgE/PrpD, N-terminal	Domain

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.