DB code: S00241

CATH domain 3.20.20.60 : TIM Barrel Catalytic domain
E.C. 4.1.3.1
CSA 1f8m
M-CSA 1f8m
MACiE M0272

CATH domain Related DB codes (homologues)
3.20.20.60 : TIM Barrel T00217 S00197 S00242 T00043 D00477

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P0A5H3 Isocitrate lyase
ICL
Isocitrase
Isocitratase
EC 4.1.3.1
NP_334893.1 (Protein)
NC_002755.2 (DNA/RNA sequence)
YP_006513796.1 (Protein)
NC_018143.1 (DNA/RNA sequence)
YP_177728.1 (Protein)
NC_000962.3 (DNA/RNA sequence)
PF00463 (ICL)
[Graphical View]
P0A9G6 Isocitrate lyase
ICL
Isocitrase
Isocitratase
EC 4.1.3.1
NP_418439.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_492158.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF00463 (ICL)
[Graphical View]

KEGG enzyme name
isocitrate lyase
isocitrase
isocitritase
isocitratase
threo-Ds-isocitrate glyoxylate-lyase
isocitrate glyoxylate-lyase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0A5H3 ACEA_MYCTU Isocitrate = succinate + glyoxylate. Homotetramer (By similarity). Cytoplasm.
P0A9G6 ACEA_ECOLI Isocitrate = succinate + glyoxylate. Homotetramer. Cytoplasm. Divalent cations.

KEGG Pathways
Map code Pathways E.C.
MAP00630 Glyoxylate and dicarboxylate metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00311 C00042 C00048
E.C.
Compound Magnesium Isocitrate Succinate Glyoxylate
Type divalent metal (Ca2+, Mg2+) carbohydrate,carboxyl group carboxyl group carbohydrate,carboxyl group
ChEBI 18420
30887
15741
16891
PubChem 888
1198
1110
21952380
760
1f61A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Unbound
1f61B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Unbound
1f8iA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Bound:SIN Bound:GLV
1f8iB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Bound:SIN Bound:GLV
1f8iC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Bound:SIN Bound:GLV
1f8iD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Bound:SIN Bound:GLV
1f8mA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Analogue:PYR
1f8mB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Analogue:PYR
1f8mC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Analogue:PYR
1f8mD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Analogue:PYR
1igwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Analogue:PYR
1igwB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Analogue:PYR
1igwC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Analogue:PYR
1igwD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain bound:_MG Unbound Unbound Analogue:PYR

Reference for Active-site residues
resource references E.C.
Swiss-prot;P28298, P0A5H3 & literature [16]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1f61A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 191 ASP 153(Magnesium binding)
1f61B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 191 ASP 153(Magnesium binding)
1f8iA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 153(Magnesium binding) mutant C191S
1f8iB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 153(Magnesium binding) mutant C191S
1f8iC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 153(Magnesium binding) mutant C191S
1f8iD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 153(Magnesium binding) mutant C191S
1f8mA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 191 ASP 153(Magnesium binding)
1f8mB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 191 ASP 153(Magnesium binding)
1f8mC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 191 ASP 153(Magnesium binding)
1f8mD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 191 ASP 153(Magnesium binding)
1igwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 195 ASP 157(Magnesium binding) invisible 196-199
1igwB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 157(Magnesium binding) invisible 195-199
1igwC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 195 ASP 157(Magnesium binding)
1igwD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 157(Magnesium binding) invisible 193-199

References for Catalytic Mechanism
References Sections No. 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]
Resource
Comments
Medline ID
PubMed ID 3767376
Journal Arch Biochem Biophys
Year 1986
Volume 250
Pages 238-48
Authors Malhotra OP, Dwivedi UN
Title 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.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 3947071
Journal Arch Biochem Biophys
Year 1986
Volume 244
Pages 85-93
Authors Pinzauti G, Giachetti E, Camici G, Manao G, Cappugi G, Vanni P
Title An isocitrate lyase of higher plants: analysis and comparison of some molecular properties.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 2947898
Journal J Bacteriol
Year 1987
Volume 169
Pages 359-66
Authors Thomas GH, Baxter RL
Title Analysis of mutational lesions of acetate metabolism in Neurospora crassa by 13C nuclear magnetic resonance.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 3345764
Journal Eur J Biochem
Year 1988
Volume 172
Pages 85-91
Authors Giachetti E, Pinzauti G, Bonaccorsi R, Vanni P
Title Isocitrate lyase from Pinus pinea. Characterization of its true substrate and the action of magnesium ions.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 2184988
Journal Comp Biochem Physiol B
Year 1990
Volume 95
Pages 431-58
Authors Vanni P, Giachetti E, Pinzauti G, McFadden BA
Title Comparative structure, function and regulation of isocitrate lyase, an important assimilatory enzyme.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 2067012
Journal J Mol Biol
Year 1991
Volume 220
Pages 13-6
Authors Abeysinghe SI, Baker PJ, Rice DW, Rodgers HF, Stillman TJ, Ko YH, McFadden BA, Nimmo HG
Title Use of chemical modification in the crystallization of isocitrate lyase from Escherichia coli.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 8954579
Journal Arch Biochem Biophys
Year 1996
Volume 336
Pages 309-15
Authors Rehman A, Mcfadden BA
Title The consequences of replacing histidine 356 in isocitrate lyase from Escherichia coli.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 8641464
Journal FEBS Lett
Year 1996
Volume 385
Pages 43-6
Authors Ordiz I, Herrero P, Rodicio R, Moreno F
Title Glucose-induced inactivation of isocitrate lyase in Saccharomyces cerevisiae is mediated by the cAMP-dependent protein kinase catalytic subunits Tpk1 and Tpk2.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 9355749
Journal Biochem J
Year 1997
Volume 327
Pages 171-6
Authors Beeckmans S, Khan AS, Van Driessche E
Title Role of Mg2+ in the structure and activity of maize (Zea mays L.) isocitrate lyase: indications for hysteretic behaviour.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 9242982
Journal Biochimie
Year 1997
Volume 79
Pages 179-86
Authors Rua J, Soler J, Busto F, de Arriaga D
Title Effect of pH on the role of Mg2+ and Mn2+ on Phycomyces isocitrate lyase kinetics.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 11543358
Journal Microgravity Sci Technol
Year 1999
Volume 12
Pages 36-40
Authors Giachetti E, Ranaldi F, Fiusco A, Tacconi M, Veratti R, Falciani P, Vanni P
Title Enzyme kinetic parameters are not altered by microgravity.
Related PDB
Related UniProtKB
[12]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID 20392544
PubMed ID 10932251
Journal Nat Struct Biol
Year 2000
Volume 7
Pages 663-8
Authors Sharma V, Sharma S, Hoener zu Bentrup K, McKinney JD, Russell DG, Jacobs WR Jr, Sacchettini JC
Title Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis.
Related PDB 1f61 1f8i 1f8m
Related UniProtKB P0A5H3
[13]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS), AND REVISIONS TO 17 AND 156.
Medline ID 20264302
PubMed ID 10801489
Journal Structure Fold Des
Year 2000
Volume 8
Pages 349-62
Authors Britton K, Langridge S, Baker PJ, Weeradechapon K, Sedelnikova SE, De Lucas JR, Rice DW, Turner G
Title The crystal structure and active site location of isocitrate lyase from the fungus Aspergillus nidulans.
Related PDB 1dqu
Related UniProtKB P28298
[14]
Resource
Comments
Medline ID
PubMed ID 11526312
Journal Acta Crystallogr D Biol Crystallogr
Year 2001
Volume 57
Pages 1209-18
Authors Britton KL, Abeysinghe IS, Baker PJ, Barynin V, Diehl P, Langridge SJ, McFadden BA, Sedelnikova SE, Stillman TJ, Weeradechapon K, Rice DW
Title The structure and domain organization of Escherichia coli isocitrate lyase.
Related PDB 1igw
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 11709206
Journal J Inorg Biochem
Year 2001
Volume 87
Pages 1-8
Authors Hamel RD, Appanna VD
Title Modulation of TCA cycle enzymes and aluminum stress in Pseudomonas fluorescens.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 12783190
Journal Curr Microbiol
Year 2003
Volume 47
Pages 32-9
Authors Appanna VD, Hamel RD, Levasseur R
Title The metabolism of aluminum citrate and biosynthesis of oxalic acid in Pseudomonas fluorescens.
Related PDB
Related UniProtKB

Comments

Created Updated
2004-05-24 2009-02-26