1MUM

Structure of the 2-Methylisocitrate Lyase (PrpB) from Escherichia coli

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1muma_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Phosphoenolpyruvate mutase/Isocitrate lyase-like	2-methylisocitrate lyase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1mumb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Phosphoenolpyruvate mutase/Isocitrate lyase-like	2-methylisocitrate lyase	(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)
A	SCOP2 Family	Phosphoenolpyruvate mutase/Isocitrate lyase-like	8020490	4003532	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Phosphoenolpyruvate/pyruvate domain	8032870	3000510	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8032870	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)
A	PEP_mutase	e1mumA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
B	PEP_mutase	e1mumB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
B	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, 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, 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	catabolic process oxoacid metabolic process short-chain fatty acid metabolic process organic acid catabolic process organic acid metabolic process cellular lipid catabolic process cellular catabolic process propionate catabolic process organic substance metabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule metabolic process propionate metabolic process fatty acid metabolic process catabolic process oxoacid metabolic process short-chain fatty acid metabolic process organic acid catabolic process organic acid metabolic process cellular lipid catabolic process cellular catabolic process propionate catabolic process organic substance metabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule metabolic process propionate metabolic process fatty acid metabolic process short-chain fatty acid catabolic process lipid catabolic process cellular metabolic process carboxylic acid metabolic process primary metabolic process fatty acid catabolic process propionate catabolic process, 2-methylcitrate cycle cellular lipid metabolic process metabolic process cellular process monocarboxylic acid metabolic process small molecule catabolic process organic substance catabolic process lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	methylisocitrate lyase M-CSA #182	Involved in the catabolism of short chain fatty acids (SCFA) via the 2-methylcitrate cycle I (propionate degradation route). Catalyses the thermodynamically favored C-C bond cleavage of (2R,3S)-2-methylisocitrate to yield pyruvate and succinate via an alpha-carboxy-carbanion intermediate.	Defined by 10 residues: TYR:A-42 [auth A-43]ASP:A-57 [auth A-58]ASP:A-84 [auth A-85]ASP:A-86 [auth A-87]HIS:A-112 [auth A-113]GLU:A-114 [auth A-115]CYS:A-122 [auth A-123]ARG:A-157 [auth A-158]GLU:A-187 [auth A-188]ASN:A-209 [auth A-210] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.1.3.30 (PDB Primary Data) Search M-CSA Motif + EC 4.1.3.30

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.