6T5M | pdb_00006t5m

Crystal structure of 2-methylisocitrate lyase (PrpB) from Pseudomonas aeruginosa in complex with Mg(II)-pyruvate.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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)
D [auth B]	d6t5mb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Phosphoenolpyruvate mutase/Isocitrate lyase-like	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
C [auth D]	d6t5md_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Phosphoenolpyruvate mutase/Isocitrate lyase-like	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
B [auth A]	d6t5ma_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Phosphoenolpyruvate mutase/Isocitrate lyase-like	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
A [auth C]	d6t5mc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Phosphoenolpyruvate mutase/Isocitrate lyase-like	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth B]	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8100534	3000510	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8100534	3000510	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8100534	3000510	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8100534	3000510	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)
D [auth B]	Metallophos_2	e6t5mB1	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: Metallophos_2	ECOD (v294.1)
C [auth D]	Metallophos_2	e6t5mD1	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: Metallophos_2	ECOD (v294.1)
B [auth A]	Metallophos_2	e6t5mA1	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: Metallophos_2	ECOD (v294.1)
A [auth C]	Metallophos_2	e6t5mC1	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: Metallophos_2	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], B [auth A], C [auth D], D [auth B]	PF13714	Phosphoenolpyruvate phosphomutase (PEP_mutase)	Phosphoenolpyruvate phosphomutase	This domain includes the enzyme Phosphoenolpyruvate phosphomutase (EC:5.4.2.9). This protein Swiss:O86937 has been characterised as catalysing the formation of a carbon-phosphorus bond by converting phosphoenolpyruvate (PEP) to phosphonopyruvate (P-P ...	This domain includes the enzyme Phosphoenolpyruvate phosphomutase (EC:5.4.2.9). This protein Swiss:O86937 has been characterised as catalysing the formation of a carbon-phosphorus bond by converting phosphoenolpyruvate (PEP) to phosphonopyruvate (P-Pyr) [1]. This enzyme has a TIM barrel fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth A], C [auth D], D [auth B]	2-methylisocitrate lyase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding oxo-acid-lyase activity methylisocitrate lyase activity lyase activity catalytic activity carbon-carbon lyase activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], B [auth A], C [auth D], D [auth B]	IPR015813	Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily	Homologous Superfamily
A [auth C], B [auth A], C [auth D], D [auth B]	IPR018523	Isocitrate lyase/phosphorylmutase, conserved site	Conserved Site
A [auth C], B [auth A], C [auth D], D [auth B]	IPR012695	2-methylisocitrate lyase	Family
A [auth C], B [auth A], C [auth D], D [auth B]	IPR039556	ICL/PEPM domain	Domain
A [auth C], B [auth A], C [auth D], D [auth B]	IPR040442	Pyruvate kinase-like domain superfamily	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.