6S62 | pdb_00006s62

Crystal structure of 2-methylcitrate dehydratase (PrpD) from Pseudomonas aeruginosa in apo form.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
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)
F	d6s62f_	Multi-domain proteins (alpha and beta)	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
E	d6s62e_	Multi-domain proteins (alpha and beta)	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
D	d6s62d_	Multi-domain proteins (alpha and beta)	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
C	d6s62c_	Multi-domain proteins (alpha and beta)	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
B	d6s62b_	Multi-domain proteins (alpha and beta)	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
A	d6s62a_	Multi-domain proteins (alpha and beta)	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F		e6s62F1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F:	ECOD (v294.1)
E		e6s62E1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F:	ECOD (v294.1)
D		e6s62D1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F:	ECOD (v294.1)
C		e6s62C1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F:	ECOD (v294.1)
B		e6s62B1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F:	ECOD (v294.1)
A		e6s62A1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F:	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, 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, B, C, D, E A, B, C, D, E, 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, B, C, D, E A, B, C, D, E, F	Propionate catabolic protein PrpD	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding 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 monocarboxylic acid metabolic process propionate metabolic process lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR005656	MmgE/PrpD	Family
A, B, C, D, E A, B, C, D, E, F	IPR036148	MmgE/PrpD superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR042188	MmgE/PrpD superfamily, domain 2	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR042183	MmgE/PrpD superfamily, domain 1	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR045337	MmgE/PrpD, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR012705	2-methylcitrate dehydratase PrpD	Family
A, B, C, D, E A, B, C, D, E, 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.