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Search The CSA
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Catalytic Site Atlas

CSA LITERATURE entry for 1fgh

E.C. nameaconitate hydratase
SpeciesBos taurus (Bovine)
E.C. Number (IntEnz) 4.2.1.3
CSA Homologues of 1fghThere are 20 Homologs
CSA Entries With UniProtID P20004
CSA Entries With EC Number 4.2.1.3
PDBe Entry 1fgh
PDBSum Entry 1fgh
MACiE Entry 1fgh

Literature Report

IntroductionAconitase (Aconitate hydratase) contains an Fe-S cluster within the active site. This can be in the form 4Fe-4S in which case the enzyme functions as an aconitate hydratase, performing the dehydration-rehydration of citrate to isocitrate via cis-aconitate in the second and third steps of the Krebs cycle. When the Fe-S cluster is in the form 3Fe-4S (cytosolic aconitase) the enzyme functions as an Iron Regulatory Protein (IRP) which binds to a conserved sequence (Iron Responsive Element; IRE) in mRNAs encoding proteins that function in the maintenance of iron homeostasis thus regulating the translation of that mRNA. Aconitase occurs in bacteria, plants, animals and fungi in mitochondrial and cytosolic forms.
MechansimSer642, the general base is thought to be deprotonated when the isocitrate substrate binds to the Fe centre and Fe-OH2 is formed in the coordination sphere. Serine 642 abstracts the proton from the beta-carbon of isocitrate to form cis-aconitate. Conjugate elimination of the hydroxyl group and cleavage of the alpha C-OH bond results in the deprotonation of His101. The His101-Asp100 pair activate the Fe coordinated water molecule to provide a hydroxide to cis-aconitate. Ser642 then protonates the alpha carbon of this intermediate to form citrate.
Reaction

Catalytic Sites for 1fgh

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
SerA642669macie:sideChainThe residue undergoes rapid proton exchange on binding of the substrate and water to the Fe metal centre. In the ionised form the residue then acts as a general base towards isocitrate, abstracting the beta-carbon proton. After elimination and reinsertion of water, Ser642 acts as a general acid to the alpha carbon of the cis-aconitate intermediate, forming the citrate product.
HisA101128macie:sideChainThe residue acts as a general acid to the eliminated hydroxyl from isocitrate. Hydrogen bonding with Asp100 stabilises the residue's positive charge.
AspA100127macie:sideChainThe residue stabilises the positive charge on His101, facilitating the the role of His101 as a general acid.
AspA165192macie:sideChainThe residue hydrogen bonds to both the hydroxyl group of the isocitrate and the coordinated hydroxide. This allows Asp165 to orientate the substrate correctly within the metal coordination sphere for catalysis.
ArgA447474macie:sideChainThe interaction between the residue's gaunidinium group and one of the substrate carboxylates enhances the active site specificity for substrates structure and stereochemistry.
ArgA644671macie:mainChainAmideThe residue's backbone amide stabilises the alkoxide transition state in the elimination of OH from the isocitrate substrate.

Literature References

Notes:
Zheng L
Mutational analysis of active site residues in pig heart aconitase.
J Biol Chem 1992 267 7895-7903
PubMed: 1313811
Irvin SD
A unique fungal lysine biosynthesis enzyme shares a common ancestor with tricarboxylic acid cycle and leucine biosynthetic enzymes found in diverse organisms.
J Mol Evol 1998 46 401-408
PubMed: 9541534
Lauble H
Crystal structures of aconitase with isocitrate and nitroisocitrate bound.
Biochemistry 1992 31 2735-2748
PubMed: 1547214
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