3I4E | pdb_00003i4e

Crystal structure of Isocitrate Lyase from Burkholderia pseudomallei

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)
D	d3i4ed_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Phosphoenolpyruvate mutase/Isocitrate lyase-like	automated matches	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)
C	d3i4ec_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Phosphoenolpyruvate mutase/Isocitrate lyase-like	automated matches	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)
B	d3i4eb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Phosphoenolpyruvate mutase/Isocitrate lyase-like	automated matches	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)
A	d3i4ea_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Phosphoenolpyruvate mutase/Isocitrate lyase-like	automated matches	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8075313	3000510	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8075313	3000510	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8075313	3000510	SCOP2B (2022-06-29)
A	SCOP2 Family	Phosphoenolpyruvate mutase/Isocitrate lyase-like	8075312	4003532	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Phosphoenolpyruvate/pyruvate domain	8075313	3000510	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)
D	Ribosomal_L36	e3i4eD1	A: alpha bundles	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: Ribosomal_L36	ECOD (develop294)
C	Ribosomal_L36	e3i4eC1	A: alpha bundles	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: Ribosomal_L36	ECOD (develop294)
B	Ribosomal_L36	e3i4eB1	A: alpha bundles	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: Ribosomal_L36	ECOD (develop294)
A	V-set	e3i4eA1	A: alpha bundles	X: Alpha-beta plaits	H: HMA-related	T: HMA, heavy metal-associated domain	F: V-set	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
C	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)
A	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, C, D	PF00463	Isocitrate lyase family (ICL)	Isocitrate lyase family		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Isocitrate lyase	isocitrate lyase activity oxo-acid-lyase activity lyase activity catalytic activity carbon-carbon lyase activity cation binding ion binding binding metal ion binding small molecule binding	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 carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process organic acid 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 carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process aldehyde metabolic process small molecule metabolic process monocarboxylic acid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR015813	Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR018523	Isocitrate lyase/phosphorylmutase, conserved site	Conserved Site
A, B, C, D	IPR039556	ICL/PEPM domain	Domain
A, B, C, D	IPR040442	Pyruvate kinase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR006254	Isocitrate lyase	Family

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.