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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1p1x
Original Entry
Title:
Lyase
Compound:
Deoxyribose-phosphate aldolase
Mutant:
No
UniProt/Swiss-Prot:
P00882-DEOC_ECOLI
EC Class:
4.1.2.4
Other CSA Entries:
Overview of all sites for 1p1x
Homologues of 1p1x
Entries for UniProt/Swiss-Prot: P00882
Entries for EC: 4.1.2.4
Other Databases:
PDB entry: 1p1x
PDBsum entry: 1p1x
UniProt/Swiss-Prot: P00882
IntEnz entry: 4.1.2.4
Literature Report:
Introduction:
The class I aldolase Deoxyribose-5-phosphate aldolase from E.coli is able to catalyse the formation of DRP from acetaldehyde and glyceraldehyde-3-phosphate. As such is it a rare form of class I aldolase as it is able to catalyse the condensation between two aldehydes rather than an aldehyde and a ketone.
Mechanism:
The reaction proceeds via initial nucleophilic attack by Lys 167 on acetaldehyde to form a Schiff base intermediate; deprotonation of the Lys 167 by Asp 102 facilitates this. Subsequent deprotonation of the C2 of the acetaldehyde by a Lys 201 activated water molecule (Wat29) results in the production of a nucleophilic carbon centre which attacks the G3P molecule to form the linear form of the product, DRP.
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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
2029 0
Acid/baseSubstrate
Acts as the general acid-base for deprotonation at C2 of the Schiff base intermediate and protonation of the carbonyl oxygen of G3P to allow the product to form.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11598300 Current protein Conservation of residue
PubMed ID 11598300 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 102 102Sidechain
Acid/baseResidue
Acid/baseWater
Activates Lys 167 towards nucleophilic attack so that Schiff base intermediate can be formed. Also acts to protonate and deprotonate the Lys 167 in order to allow collapse of the Schiff base intermediate. Furthermore, activates water as part of proton relay system with Lys 201.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11598300 Current protein Conservation of residue
PubMed ID 11598300 Current protein Mutagenesis of residue
PubMed ID 11598300 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
LYSA 167 167Sidechain
NucleophileSubstrate
Attacks electrophilic carbon centre to form Schiff base intermediate.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11598300 Current protein pH dependence of reaction
PubMed ID 11598300 Current protein Residue is covalently bound to intermediate, based on structural data
PubMed ID 11598300 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
LYSA 201 201Sidechain
ElectrostaticResidue
ElectrostaticWater
Activates water to allow it to act as a general acid base for deprotonation at C2 of the Schiff base intermediate. Also activates Lys 167 towards nucleophilic attack.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11598300 Current protein Conservation of residue
PubMed ID 11598300 Current protein Mutagenesis of residue
PubMed ID 11598300 Current protein Residue is positioned appropriately (ligand position known)
References:
1
Observation of covalent intermediates in an enzyme mechanism at atomic resolution.
A. Heine and G. DeSantis and J. G. Luz and M. Mitchell and C. H. Wong and I. A. Wilson
Science 294, (5541) 369-74, (2001).
11598300
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