S00241
type: Enzyme
cath: TIM Barrel
ec: https://purl.uniprot.org/enzyme/4.1.3.1
csa: 1f8m
macie: M0272
uniprot: P0A5H3
uniprot: P0A9G6
kegg enzyme: isocitrate lyase
kegg enzyme: isocitrase
kegg enzyme: isocitritase
kegg enzyme: isocitratase
kegg enzyme: threo-Ds-isocitrate glyoxylate-lyase
kegg enzyme: isocitrate glyoxylate-lyase
kegg pathway: Glyoxylate and dicarboxylate metabolism
kegg cofactor: Magnesium
kegg substrate: Isocitrate
kegg product: Succinate
kegg product: Glyoxylate
pdb: 1f61A
pdb: 1f61B
pdb: 1f8iA
pdb: 1f8iB
pdb: 1f8iC
pdb: 1f8iD
pdb: 1f8mA
pdb: 1f8mB
pdb: 1f8mC
pdb: 1f8mD
pdb: 1igwA
pdb: 1igwB
pdb: 1igwC
pdb: 1igwD
pdb bound state: Unbound
  compound: Isocitrate
  pdb: 1f61A
pdb bound state: Unbound
  compound: Isocitrate
  pdb: 1f61B
pdb bound state: Unbound
  compound: Isocitrate
  pdb: 1f8iA
pdb bound state: Unbound
  compound: Isocitrate
  pdb: 1f8iB
pdb bound state: Unbound
  compound: Isocitrate
  pdb: 1f8iC
pdb bound state: Unbound
  compound: Isocitrate
  pdb: 1f8iD
pdb bound state: Unbound
  compound: Isocitrate
  pdb: 1f8mA
pdb bound state: Unbound
  compound: Isocitrate
  pdb: 1f8mB
pdb bound state: Unbound
  compound: Isocitrate
  pdb: 1f8mC
pdb bound state: Unbound
  compound: Isocitrate
  pdb: 1f8mD
pdb bound state: Unbound
  compound: Isocitrate
  pdb: 1igwA
pdb bound state: Unbound
  compound: Isocitrate
  pdb: 1igwB
pdb bound state: Unbound
  compound: Isocitrate
  pdb: 1igwC
pdb bound state: Unbound
  compound: Isocitrate
  pdb: 1igwD
pdb bound state: Bound
  compound: Magnesium
  pdb: 1igwD
  ligand het code: _MG
pdb bound state: Unbound
  compound: Succinate
  pdb: 1f61A
pdb bound state: Unbound
  compound: Succinate
  pdb: 1f61B
pdb bound state: Unbound
  compound: Succinate
  pdb: 1f8mA
pdb bound state: Unbound
  compound: Succinate
  pdb: 1f8mB
pdb bound state: Unbound
  compound: Succinate
  pdb: 1f8mC
pdb bound state: Unbound
  compound: Succinate
  pdb: 1f8mD
pdb bound state: Unbound
  compound: Succinate
  pdb: 1igwA
pdb bound state: Unbound
  compound: Succinate
  pdb: 1igwB
pdb bound state: Unbound
  compound: Succinate
  pdb: 1igwC
pdb bound state: Unbound
  compound: Succinate
  pdb: 1igwD
pdb bound state: Unbound
  compound: Glyoxylate
  pdb: 1f61A
pdb bound state: Unbound
  compound: Glyoxylate
  pdb: 1f61B
pdb bound state: Analogue
  compound: Glyoxylate
  pdb: 1f8mA
  ligand het code: PYR
pdb bound state: Analogue
  compound: Glyoxylate
  pdb: 1f8mB
  ligand het code: PYR
active site residues resources: http://ezcatdb.cbrc.jp/EzCatDB/reference/S00241#17
active site residues resources: P28298
active site residues resources: P0A5H3
references: Formation of enzyme-bound carbanion intermediate in the isocitrate lyase-catalyzed reaction: enzymatic reaction of tetranitromethane with substrates and its dependence on effector, pH, and metal ions.
references: An isocitrate lyase of higher plants: analysis and comparison of some molecular properties.
references: Analysis of mutational lesions of acetate metabolism in Neurospora crassa by 13C nuclear magnetic resonance.
references: Isocitrate lyase from Pinus pinea. Characterization of its true substrate and the action of magnesium ions.
references: Comparative structure, function and regulation of isocitrate lyase, an important assimilatory enzyme.
references: Use of chemical modification in the crystallization of isocitrate lyase from Escherichia coli.
references: The consequences of replacing histidine 356 in isocitrate lyase from Escherichia coli.
references: Glucose-induced inactivation of isocitrate lyase in Saccharomyces cerevisiae is mediated by the cAMP-dependent protein kinase catalytic subunits Tpk1 and Tpk2.
references: Role of Mg2+ in the structure and activity of maize (Zea mays L.) isocitrate lyase: indications for hysteretic behaviour.
references: Effect of pH on the role of Mg2+ and Mn2+ on Phycomyces isocitrate lyase kinetics.
references: Enzyme kinetic parameters are not altered by microgravity.
references: Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis.
references: The crystal structure and active site location of isocitrate lyase from the fungus Aspergillus nidulans.
references: The structure and domain organization of Escherichia coli isocitrate lyase.
references: Modulation of TCA cycle enzymes and aluminum stress in Pseudomonas fluorescens.
references: The metabolism of aluminum citrate and biosynthesis of oxalic acid in Pseudomonas fluorescens.

TIM Barrel
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.20.20.60
catalytic domain: index.html

Glyoxylate and dicarboxylate metabolism
type: KeggPathway
references: KEGG:MAP00630

Magnesium
type: KeggCofactor
references: KEGG:C00305
compound type: divalent metal (Ca2+, Mg2+)
references: CHEBI:18420
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Isocitrate
type: KeggSubstrate
references: KEGG:C00311
compound type: carbohydrate
compound type: carboxyl group
references: CHEBI:30887
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Succinate
type: KeggProduct
references: KEGG:C00042
compound type: carboxyl group
references: CHEBI:15741
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Glyoxylate
type: KeggProduct
references: KEGG:C00048
compound type: carbohydrate
compound type: carboxyl group
references: CHEBI:16891
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

1f61A
type: Pdb
references: 1f61
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1f61
catalytic residue: CYS 191
cofactor binding residue: ASP 153(Magnesium binding)

1f61B
type: Pdb
references: 1f61
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1f61
catalytic residue: CYS 191
cofactor binding residue: ASP 153(Magnesium binding)

1f8iA
type: Pdb
references: 1f8i
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1f8i
cofactor binding residue: ASP 153(Magnesium binding)
comment: mutant C191S

1f8iB
type: Pdb
references: 1f8i
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1f8i
cofactor binding residue: ASP 153(Magnesium binding)
comment: mutant C191S

1f8iC
type: Pdb
references: 1f8i
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1f8i
cofactor binding residue: ASP 153(Magnesium binding)
comment: mutant C191S

1f8iD
type: Pdb
references: 1f8i
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1f8i
cofactor binding residue: ASP 153(Magnesium binding)
comment: mutant C191S

1f8mA
type: Pdb
references: 1f8m
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1f8m
catalytic residue: CYS 191
cofactor binding residue: ASP 153(Magnesium binding)

1f8mB
type: Pdb
references: 1f8m
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1f8m
catalytic residue: CYS 191
cofactor binding residue: ASP 153(Magnesium binding)

1f8mC
type: Pdb
references: 1f8m
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1f8m
catalytic residue: CYS 191
cofactor binding residue: ASP 153(Magnesium binding)

1f8mD
type: Pdb
references: 1f8m
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1f8m
catalytic residue: CYS 191
cofactor binding residue: ASP 153(Magnesium binding)

1igwA
type: Pdb
references: 1igw
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1igw
catalytic residue: CYS 195
cofactor binding residue: ASP 157(Magnesium binding)
comment: invisible 196-199

1igwB
type: Pdb
references: 1igw
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1igw
cofactor binding residue: ASP 157(Magnesium binding)
comment: invisible 195-199

1igwC
type: Pdb
references: 1igw
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1igw
catalytic residue: CYS 195
cofactor binding residue: ASP 157(Magnesium binding)

1igwD
type: Pdb
references: 1igw
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1igw
cofactor binding residue: ASP 157(Magnesium binding)
comment: invisible 193-199

Formation of enzyme-bound carbanion intermediate in the isocitrate lyase-catalyzed reaction: enzymatic reaction of tetranitromethane with substrates and its dependence on effector, pH, and metal ions.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/3767376
journal: Arch Biochem Biophys
volume: 250
pages: 238-48
published year: 1986
authors:
  item: Malhotra OP
  item: Dwivedi UN

An isocitrate lyase of higher plants: analysis and comparison of some molecular properties.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/3947071
journal: Arch Biochem Biophys
volume: 244
pages: 85-93
published year: 1986
authors:
  item: Pinzauti G
  item: Giachetti E
  item: Camici G
  item: Manao G
  item: Cappugi G
  item: Vanni P

Analysis of mutational lesions of acetate metabolism in Neurospora crassa by 13C nuclear magnetic resonance.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/2947898
journal: J Bacteriol
volume: 169
pages: 359-66
published year: 1987
authors:
  item: Thomas GH
  item: Baxter RL

Isocitrate lyase from Pinus pinea. Characterization of its true substrate and the action of magnesium ions.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/3345764
journal: Eur J Biochem
volume: 172
pages: 85-91
published year: 1988
authors:
  item: Giachetti E
  item: Pinzauti G
  item: Bonaccorsi R
  item: Vanni P

Comparative structure, function and regulation of isocitrate lyase, an important assimilatory enzyme.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/2184988
journal: Comp Biochem Physiol B
volume: 95
pages: 431-58
published year: 1990
authors:
  item: Vanni P
  item: Giachetti E
  item: Pinzauti G
  item: McFadden BA

Use of chemical modification in the crystallization of isocitrate lyase from Escherichia coli.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/2067012
journal: J Mol Biol
volume: 220
pages: 13-6
published year: 1991
authors:
  item: Abeysinghe SI
  item: Baker PJ
  item: Rice DW
  item: Rodgers HF
  item: Stillman TJ
  item: Ko YH
  item: McFadden BA
  item: Nimmo HG

The consequences of replacing histidine 356 in isocitrate lyase from Escherichia coli.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8954579
journal: Arch Biochem Biophys
volume: 336
pages: 309-15
published year: 1996
authors:
  item: Rehman A
  item: Mcfadden BA

Glucose-induced inactivation of isocitrate lyase in Saccharomyces cerevisiae is mediated by the cAMP-dependent protein kinase catalytic subunits Tpk1 and Tpk2.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8641464
journal: FEBS Lett
volume: 385
pages: 43-6
published year: 1996
authors:
  item: Ordiz I
  item: Herrero P
  item: Rodicio R
  item: Moreno F

Role of Mg2+ in the structure and activity of maize (Zea mays L.) isocitrate lyase: indications for hysteretic behaviour.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9355749
journal: Biochem J
volume: 327
pages: 171-6
published year: 1997
authors:
  item: Beeckmans S
  item: Khan AS
  item: Van Driessche E

Effect of pH on the role of Mg2+ and Mn2+ on Phycomyces isocitrate lyase kinetics.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9242982
journal: Biochimie
volume: 79
pages: 179-86
published year: 1997
authors:
  item: Rua J
  item: Soler J
  item: Busto F
  item: de Arriaga D

Enzyme kinetic parameters are not altered by microgravity.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11543358
journal: Microgravity Sci Technol
volume: 12
pages: 36-40
published year: 1999
authors:
  item: Giachetti E
  item: Ranaldi F
  item: Fiusco A
  item: Tacconi M
  item: Veratti R
  item: Falciani P
  item: Vanni P

Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
medline id: 20392544
references: http://www.ncbi.nlm.nih.gov/pubmed/10932251
journal: Nat Struct Biol
volume: 7
pages: 663-8
published year: 2000
authors:
  item: Sharma V
  item: Sharma S
  item: Hoener zu Bentrup K
  item: McKinney JD
  item: Russell DG
  item: Jacobs WR Jr
  item: Sacchettini JC
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P0A5H3

The crystal structure and active site location of isocitrate lyase from the fungus Aspergillus nidulans.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS), AND REVISIONS TO 17 AND 156.
medline id: 20264302
references: http://www.ncbi.nlm.nih.gov/pubmed/10801489
journal: Structure Fold Des
volume: 8
pages: 349-62
published year: 2000
authors:
  item: Britton K
  item: Langridge S
  item: Baker PJ
  item: Weeradechapon K
  item: Sedelnikova SE
  item: De Lucas JR
  item: Rice DW
  item: Turner G
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P28298

The structure and domain organization of Escherichia coli isocitrate lyase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11526312
journal: Acta Crystallogr D Biol Crystallogr
volume: 57
pages: 1209-18
published year: 2001
authors:
  item: Britton KL
  item: Abeysinghe IS
  item: Baker PJ
  item: Barynin V
  item: Diehl P
  item: Langridge SJ
  item: McFadden BA
  item: Sedelnikova SE
  item: Stillman TJ
  item: Weeradechapon K
  item: Rice DW
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Modulation of TCA cycle enzymes and aluminum stress in Pseudomonas fluorescens.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11709206
journal: J Inorg Biochem
volume: 87
pages: 1-8
published year: 2001
authors:
  item: Hamel RD
  item: Appanna VD

The metabolism of aluminum citrate and biosynthesis of oxalic acid in Pseudomonas fluorescens.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12783190
journal: Curr Microbiol
volume: 47
pages: 32-9
published year: 2003
authors:
  item: Appanna VD
  item: Hamel RD
  item: Levasseur R

Analogue
compound: Glyoxylate
pdb: 1f8mC
ligand het code: PYR

Analogue
compound: Glyoxylate
pdb: 1f8mD
ligand het code: PYR

Analogue
compound: Glyoxylate
pdb: 1igwA
ligand het code: PYR

Analogue
compound: Glyoxylate
pdb: 1igwB
ligand het code: PYR

Analogue
compound: Glyoxylate
pdb: 1igwC
ligand het code: PYR

Analogue
compound: Glyoxylate
pdb: 1igwD
ligand het code: PYR

ReferenceForCatalyticMechanism
reference index: 5
reference section: p.444-447, p.453-455, Fig.5

ReferenceForCatalyticMechanism
reference index: 7
reference section: p.314, Fig.3

ReferenceForCatalyticMechanism
reference index: 12
reference section: p.666

ReferenceForCatalyticMechanism
reference index: 13
reference section: p.357-360

ReferenceForCatalyticMechanism
reference index: 14
reference section: p.1216-1217