6C4C | pdb_00006c4c

Crystal structure of 3-nitropropionate modified isocitrate lyase from Mycobacterium tuberculosis with glyoxylate and pyruvate

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)
A	d6c4ca1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Phosphoenolpyruvate mutase/Isocitrate lyase-like	Isocitrate lyase	(Mycobacterium tuberculosis str. Erdman = ATCC 35801 ) [TaxId: 652616 ],	SCOPe (2.08)
A	d6c4ca2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacterium tuberculosis str. Erdman = ATCC 35801 ) [TaxId: 652616 ],	SCOPe (2.08)
B	d6c4cb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Phosphoenolpyruvate mutase/Isocitrate lyase-like	Isocitrate lyase	(Mycobacterium tuberculosis str. Erdman = ATCC 35801 ) [TaxId: 652616 ],	SCOPe (2.08)
C	d6c4cc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Phosphoenolpyruvate mutase/Isocitrate lyase-like	Isocitrate lyase	(Mycobacterium tuberculosis str. Erdman = ATCC 35801 ) [TaxId: 652616 ],	SCOPe (2.08)
D	d6c4cd_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Phosphoenolpyruvate mutase/Isocitrate lyase-like	Isocitrate lyase	(Mycobacterium tuberculosis str. Erdman = ATCC 35801 ) [TaxId: 652616 ],	SCOPe (2.08)
E	d6c4ce_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Phosphoenolpyruvate mutase/Isocitrate lyase-like	Isocitrate lyase	(Mycobacterium tuberculosis str. Erdman = ATCC 35801 ) [TaxId: 652616 ],	SCOPe (2.08)
F	d6c4cf_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Phosphoenolpyruvate mutase/Isocitrate lyase-like	Isocitrate lyase	(Mycobacterium tuberculosis str. Erdman = ATCC 35801 ) [TaxId: 652616 ],	SCOPe (2.08)
G	d6c4cg_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Phosphoenolpyruvate mutase/Isocitrate lyase-like	Isocitrate lyase	(Mycobacterium tuberculosis str. Erdman = ATCC 35801 ) [TaxId: 652616 ],	SCOPe (2.08)
H	d6c4ch_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Phosphoenolpyruvate mutase/Isocitrate lyase-like	Isocitrate lyase	(Mycobacterium tuberculosis str. Erdman = ATCC 35801 ) [TaxId: 652616 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043663	3000510	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043663	3000510	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043663	3000510	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043663	3000510	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043663	3000510	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043663	3000510	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043663	3000510	SCOP2B (2022-06-29)
H	SCOP2 Family	Phosphoenolpyruvate mutase/Isocitrate lyase-like	8097899	4003532	SCOP2 (2022-06-29)
H	SCOP2 Superfamily	Phosphoenolpyruvate/pyruvate domain	8097900	3000510	SCOP2 (2022-06-29)
H	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043663	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	e6c4cA1	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	e6c4cB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
C	PEP_mutase	e6c4cC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
D	PEP_mutase	e6c4cD1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
E	PEP_mutase	e6c4cE1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
F	PEP_mutase	e6c4cF1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
G	PEP_mutase	e6c4cG1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
H	PEP_mutase	e6c4cH1	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 (utative)
B	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (utative)
C	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (utative)
D	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (utative)
E	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (utative)
F	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (utative)
G	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (utative)
H	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	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, E A, B, C, D, E, F, G, H	Isocitrate lyase 1	oxo-acid-lyase activity methylisocitrate lyase activity lyase activity catalytic activity carbon-carbon lyase activity isocitrate lyase activity protein binding binding enzyme binding zymogen binding cation binding ion 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 secondary alcohol metabolic process isocitrate metabolic process tricarboxylic acid metabolic process alcohol metabolic process response to decreased oxygen levels cellular response to stimulus response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to chemical response to oxygen levels response to abiotic stimulus	cellular anatomical structure extracellular region intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR015813	Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR018523	Isocitrate lyase/phosphorylmutase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR040442	Pyruvate kinase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	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.