1SZQ | pdb_00001szq

Crystal Structure of 2-methylcitrate dehydratase

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	d1szqb_	Multi-domain proteins (alpha and beta)	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1szqa_	Multi-domain proteins (alpha and beta)	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	2-methylcitrate dehydratase PrpD	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Serine dehydratase alpha subunit-like	8041638	3000188	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Serine metabolism enzymes domain	8054250	3000019	SCOP2B (2022-06-29)
A	SCOP2 Family	MmgE/PrpD-like	8029259	4001645	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Serine dehydratase alpha subunit-like	8041638	3000188	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Serine metabolism enzymes domain	8054250	3000019	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		e1szqB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F:	ECOD (v294.1)
B	tRNA-synt_2	e1szqB2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: tRNA-synt_2	ECOD (v294.1)
A	MmgE_PrpD_N	e1szqA1	A: alpha arrays	X: alpha-helical domain in 2-methylcitrate dehydratase PrpD	H: alpha-helical domain in 2-methylcitrate dehydratase PrpD	T: alpha-helical domain in 2-methylcitrate dehydratase PrpD	F: MmgE_PrpD_N	ECOD (v294.1)
A	MmgE_PrpD_C	e1szqA2	A: a+b three layers	X: FwdE/GAPDH domain-like	H: Serine dehydratase beta chain-like	T: Serine dehydratase beta chain-like	F: MmgE_PrpD_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	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	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 monocarboxylic acid metabolic process propionate metabolic process lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036148	MmgE/PrpD superfamily	Homologous Superfamily
A, B	IPR012705	2-methylcitrate dehydratase PrpD	Family
A, B	IPR005656	MmgE/PrpD	Family
A, B	IPR042188	MmgE/PrpD superfamily, domain 2	Homologous Superfamily
A, B	IPR042183	MmgE/PrpD superfamily, domain 1	Homologous Superfamily
A, B	IPR045337	MmgE/PrpD, C-terminal	Domain
A, B	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.