Get   for     ? 
 Site search     ? 
Catalytic Site Atlas Version 2.2.12
Find Annotated Site: PDB code:
Swiss-Prot code:
EC number:
Help
CSA entry for 1k4l
Original Entry
Title:
Isomerase
Compound:
3,4-dihydroxy-2-butanone 4-phosphate synthase
Mutant:
No
UniProt/Swiss-Prot:
Q8TG90-Q8TG90
EC Class:
5.4.99.-
Other CSA Entries:
Overview of all sites for 1k4l
Homologues of 1k4l
Entries for UniProt/Swiss-Prot: Q8TG90
Entries for EC: 5.4.99.-
Other Databases:
PDB entry: 1k4l
PDBsum entry: 1k4l
UniProt/Swiss-Prot: Q8TG90
IntEnz entry: 5.4.99.-
Literature Report:
Introduction:
3,4-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.
Mechanism:
The 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.
Sites:

Click to Display Catalytic Site (Get help with this section)
Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
1003 0
ElectrostaticWater
ElectrostaticSubstrate
ElectrostaticTransition state
Activates the substrate, stabilises the transition state, and coordinates water for nucleophilic attack on substrate as well as coordinating water to act as a proton donor.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11827524 Current protein Computer modelling
PubMed ID 11827524 Current protein Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 11827524 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
1004 0
ElectrostaticSubstrate
ElectrostaticWater
ElectrostaticTransition state
Activates the substrate, stabilises the transition state, and coordinates water to act as a proton donor.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11827524 Current protein Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 11827524 Current protein Structural similarity to homologue of known mechanism
PubMed ID 11827524 Current protein Computer modelling

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 41 41Sidechain
Acid/baseSubstrate
Acts as a base catalyst during skeletal rearrangements.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11827524 Current protein Computer modelling
PubMed ID 11827524 Current protein Conservation of residue
PubMed ID 11827524 Current protein Residue is positioned appropriately (ligand position hypothetical)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
CYSA 66 66Sidechain
Acid/baseSubstrate
Acts as a general acid catalyst to faclitate dehydration step.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11827524 Current protein Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 11827524 Current protein Computer modelling
PubMed ID 11827524 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
TYRA 94 94Sidechain
ElectrostaticTransition state
Stabilises the transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11827524 Current protein Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 11827524 Current protein Conservation of residue
PubMed ID 11827524 Current protein Computer modelling

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 99 99Sidechain
ElectrostaticResidue
Activates His 136.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11827524 Current protein Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 11827524 Current protein Computer modelling
PubMed ID 11827524 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
HISA 136 136Sidechain
ElectrostaticTransition state
Acid/baseSubstrate
Acts as a general acid/base catalyst and stabilises the transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11827524 Current protein Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 11827524 Current protein Conservation of residue
PubMed ID 11827524 Current protein Computer modelling

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLUA 174 174Sidechain
Acid/baseSubstrate
Acts as a general acid/base catalyst.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11827524 Current protein Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 11827524 Current protein Conservation of residue
PubMed ID 11827524 Current protein Computer modelling
References:
1
Structural definition of the active site and catalytic mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase.
D. I. Liao and Y. J. Zheng and P. V. Viitanen and D. B. Jordan
Biochemistry 41, (6) 1795-806, (2002).
11827524
Which EBI biological databases are available and how do I access them? EBI Site Map