EzCatDB: S00241

DB codeS00241
CATH domainDomain 13.20.20.60Catalytic domain
E.C.4.1.3.1
CSA1f8m
MACiEM0272

CATH domainRelated DB codes (homologues)
3.20.20.60T00217,S00197,S00242,T00043,D00477

Enzyme Name
Swiss-protKEGG

P0A5H3P0A9G6
Protein nameIsocitrate lyaseIsocitrate lyaseisocitrate lyase
isocitrase
isocitritase
isocitratase
threo-Ds-isocitrate glyoxylate-lyase
isocitrate glyoxylate-lyase
SynonymsICL
Isocitratase
Isocitrase
EC 4.1.3.1
ICL
Isocitratase
Isocitrase
EC 4.1.3.1

KEGG pathways
MAP codePathways
MAP00630Glyoxylate and dicarboxylate metabolism

Swiss-prot:Accession NumberP0A5H3P0A9G6
Entry nameACEA_MYCTUACEA_ECOLI
ActivityIsocitrate = succinate + glyoxylate.Isocitrate = succinate + glyoxylate.
SubunitHomotetramer (By similarity).Homotetramer.
Subcellular locationCytoplasm.Cytoplasm.
Cofactor
Divalent cations.


CofactorsSubstratesProducts
KEGG-idC00305C00311C00042C00048
CompoundMagnesiumIsocitrateSuccinateGlyoxylate
Typedivalent metal (Ca2+, Mg2+)carbohydrate,carboxyl groupcarboxyl groupcarbohydrate,carboxyl group
1f61ABound:_MGUnboundUnboundUnbound
1f61BBound:_MGUnboundUnboundUnbound
1f8iABound:_MGUnboundBound:SINBound:GLV
1f8iBBound:_MGUnboundBound:SINBound:GLV
1f8iCBound:_MGUnboundBound:SINBound:GLV
1f8iDBound:_MGUnboundBound:SINBound:GLV
1f8mABound:_MGUnboundUnboundAnalogue:PYR
1f8mBBound:_MGUnboundUnboundAnalogue:PYR
1f8mCBound:_MGUnboundUnboundAnalogue:PYR
1f8mDBound:_MGUnboundUnboundAnalogue:PYR
1igwABound:_MGUnboundUnboundAnalogue:PYR
1igwBBound:_MGUnboundUnboundAnalogue:PYR
1igwCBound:_MGUnboundUnboundAnalogue:PYR
1igwDbound:_MGUnboundUnboundAnalogue:PYR

Active-site residues
resource
Swiss-prot;P28298, P0A5H3 & literature [16]
pdbCatalytic residuesCofactor-binding residuescomment
1f61ACYS 191
ASP 153(Magnesium binding)

1f61BCYS 191
ASP 153(Magnesium binding)

1f8iA       
ASP 153(Magnesium binding)
mutant C191S
1f8iB       
ASP 153(Magnesium binding)
mutant C191S
1f8iC       
ASP 153(Magnesium binding)
mutant C191S
1f8iD       
ASP 153(Magnesium binding)
mutant C191S
1f8mACYS 191
ASP 153(Magnesium binding)

1f8mBCYS 191
ASP 153(Magnesium binding)

1f8mCCYS 191
ASP 153(Magnesium binding)

1f8mDCYS 191
ASP 153(Magnesium binding)

1igwACYS 195
ASP 157(Magnesium binding)
invisible 196-199
1igwB       
ASP 157(Magnesium binding)
invisible 195-199
1igwCCYS 195
ASP 157(Magnesium binding)

1igwD       
ASP 157(Magnesium binding)
invisible 193-199

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[5]p.444-447, p.453-455, Fig.5
[7]p.314, Fig.3
[12]p.666
[13]p.357-360
[14]p.1216-1217

references
[1]
PubMed ID3767376
JournalArch Biochem Biophys
Year1986
Volume250
Pages238-48
AuthorsMalhotra OP, Dwivedi UN
TitleFormation 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.
[2]
PubMed ID3947071
JournalArch Biochem Biophys
Year1986
Volume244
Pages85-93
AuthorsPinzauti G, Giachetti E, Camici G, Manao G, Cappugi G, Vanni P
TitleAn isocitrate lyase of higher plants: analysis and comparison of some molecular properties.
[3]
PubMed ID2947898
JournalJ Bacteriol
Year1987
Volume169
Pages359-66
AuthorsThomas GH, Baxter RL
TitleAnalysis of mutational lesions of acetate metabolism in Neurospora crassa by 13C nuclear magnetic resonance.
[4]
PubMed ID3345764
JournalEur J Biochem
Year1988
Volume172
Pages85-91
AuthorsGiachetti E, Pinzauti G, Bonaccorsi R, Vanni P
TitleIsocitrate lyase from Pinus pinea. Characterization of its true substrate and the action of magnesium ions.
[5]
PubMed ID2184988
JournalComp Biochem Physiol B
Year1990
Volume95
Pages431-58
AuthorsVanni P, Giachetti E, Pinzauti G, McFadden BA
TitleComparative structure, function and regulation of isocitrate lyase, an important assimilatory enzyme.
[6]
PubMed ID2067012
JournalJ Mol Biol
Year1991
Volume220
Pages13-6
AuthorsAbeysinghe SI, Baker PJ, Rice DW, Rodgers HF, Stillman TJ, Ko YH, McFadden BA, Nimmo HG
TitleUse of chemical modification in the crystallization of isocitrate lyase from Escherichia coli.
[7]
PubMed ID8954579
JournalArch Biochem Biophys
Year1996
Volume336
Pages309-15
AuthorsRehman A, Mcfadden BA
TitleThe consequences of replacing histidine 356 in isocitrate lyase from Escherichia coli.
[8]
PubMed ID8641464
JournalFEBS Lett
Year1996
Volume385
Pages43-6
AuthorsOrdiz I, Herrero P, Rodicio R, Moreno F
TitleGlucose-induced inactivation of isocitrate lyase in Saccharomyces cerevisiae is mediated by the cAMP-dependent protein kinase catalytic subunits Tpk1 and Tpk2.
[9]
PubMed ID9355749
JournalBiochem J
Year1997
Volume327
Pages171-6
AuthorsBeeckmans S, Khan AS, Van Driessche E
TitleRole of Mg2+ in the structure and activity of maize (Zea mays L.) isocitrate lyase: indications for hysteretic behaviour.
[10]
PubMed ID9242982
JournalBiochimie
Year1997
Volume79
Pages179-86
AuthorsRua J, Soler J, Busto F, de Arriaga D
TitleEffect of pH on the role of Mg2+ and Mn2+ on Phycomyces isocitrate lyase kinetics.
[11]
PubMed ID11543358
JournalMicrogravity Sci Technol
Year1999
Volume12
Pages36-40
AuthorsGiachetti E, Ranaldi F, Fiusco A, Tacconi M, Veratti R, Falciani P, Vanni P
TitleEnzyme kinetic parameters are not altered by microgravity.
[12]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID20392544
PubMed ID10932251
JournalNat Struct Biol
Year2000
Volume7
Pages663-8
AuthorsSharma V, Sharma S, Hoener zu Bentrup K, McKinney JD, Russell DG, Jacobs WR Jr, Sacchettini JC
TitleStructure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis.
Related PDB1f61,1f8i,1f8m
Related Swiss-protP0A5H3
[13]
CommentsX-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS), AND REVISIONS TO 17 AND 156.
Medline ID20264302
PubMed ID10801489
JournalStructure Fold Des
Year2000
Volume8
Pages349-62
AuthorsBritton K, Langridge S, Baker PJ, Weeradechapon K, Sedelnikova SE, De Lucas JR, Rice DW, Turner G
TitleThe crystal structure and active site location of isocitrate lyase from the fungus Aspergillus nidulans.
Related PDB1dqu
Related Swiss-protP28298
[14]
PubMed ID11526312
JournalActa Crystallogr D Biol Crystallogr
Year2001
Volume57
Pages1209-18
AuthorsBritton KL, Abeysinghe IS, Baker PJ, Barynin V, Diehl P, Langridge SJ, McFadden BA, Sedelnikova SE, Stillman TJ, Weeradechapon K, Rice DW
TitleThe structure and domain organization of Escherichia coli isocitrate lyase.
Related PDB1igw
[15]
PubMed ID11709206
JournalJ Inorg Biochem
Year2001
Volume87
Pages1-8
AuthorsHamel RD, Appanna VD
TitleModulation of TCA cycle enzymes and aluminum stress in Pseudomonas fluorescens.
[16]
PubMed ID12783190
JournalCurr Microbiol
Year2003
Volume47
Pages32-9
AuthorsAppanna VD, Hamel RD, Levasseur R
TitleThe metabolism of aluminum citrate and biosynthesis of oxalic acid in Pseudomonas fluorescens.


createdupdated
2004-05-242009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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