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Search The CSA
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Catalytic Site Atlas

CSA LITERATURE entry for 1k4l

E.C. name3,4-dihydroxy-2-butanone-4-phosphate synthase
SpeciesMagnaporthe grisea ()
E.C. Number (IntEnz) 4.1.99.12
CSA Homologues of 1k4l1k49,1k4i,1k4o,1k4p,1tks,1tku,2ris,2riu,
CSA Entries With UniProtID Q8TG90
CSA Entries With EC Number 4.1.99.12
PDBe Entry 1k4l
PDBSum Entry 1k4l
MACiE Entry 1k4l

Literature Report

Introduction3,4-Dihydroxy-2-butanone-4-phosphate synthase catalyses conversion of ribulose 5-phosphate to L-3,4-dihydroxy-2-butanone-4-phosphate and formate in a commitment step of riboflavin biosynthesis. This enzyme has a requirement for divalent metal cations.
MechansimThe initial enolisation step occurs with Glu 174 acting as a general base catalyst in concert with His 136 (stabilised by Asp 99) acting as a general acid catalyst. The C3 hydroxyl of the substrate is activated to become acidic by binding both metal ions and deprotonation may occur before or after the enolisation. The enolate ion is stabilised by the magnesium ions, His 136, and Tyr 94. Collapse of the intermediate and dehydration is facilitated by Cys 66 acting as a general acid catalyst. An acid-base catalysed ketonisation process follows whereby the C2 hydroxyl is deprotonated by the His 136-Asp 99 dyad and the C1 is protonated by Glu 174. 1,2-skeleton rearrangement occurs by deprotonation of the C4 hydroxyl by Asp 41. A water activated by one magnesium ion acts as a nucleophile to hydrate the substrate and proton donation by His 136 yields the enolate form of 3,4-dihydroxy-2-butanone-4-phosphate. Loss of the formate results in a shift in coordination which allows a water molecule associated to both magnesium ions to act as a proton donor in concert with Glu 174 acting as a general base catalyst to generate the final product.
Reaction

Catalytic Sites for 1k4l

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisA136136macie:sideChainActs as a general acid/base catalyst and stabilises the transition state.
GluA174174macie:sideChainActs as a general acid/base catalyst.
AspA9999macie:sideChainActivates His 136.
CysA6666macie:sideChainActs as a general acid catalyst to faclitate dehydration step.
TyrA9494macie:sideChainStabilises the transition state.
AspA4141macie:sideChainActs as a base catalyst during skeletal rearrangements.

Literature References

Notes:
Liao DI
Structural definition of the active site and catalytic mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase.
Biochemistry 2002 41 1795-1806
PubMed: 11827524
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