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Search The CSA
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Catalytic Site Atlas

CSA LITERATURE entry for 1t0u

E.C. nameuridine phosphorylase
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) 2.4.2.3
CSA Homologues of 1t0uThere are 38 Homologs
CSA Entries With UniProtID P12758
CSA Entries With EC Number 2.4.2.3
PDBe Entry 1t0u
PDBSum Entry 1t0u
MACiE Entry 1t0u

Literature Report

IntroductionThe enzyme uridine phosphorylase is very important in the pathway whereby uracil can be scavenged to increase blood uracil levels. The overall reaction thus results in the formation of ribose-1-phosphate in addition to uracil. The pathway is of particular interest because it provides a mechanism whereby the effect of base analogues such as 5BU can be minimised, thus may provide some defence against tumour formation. The enzyme itself shows significant homology to Purine nucleotide phosphorylases rather than to pyrimidine nucleotide phosphorylases, posing interesting questions about its evolution.
MechansimThe reaction mechanism is believed to be similar to that of purine nucleotide phosphorylase, so involves an carboxenium ion transition state formed through electron density from the 4' oxygen being pushed onto the 1' Carbon of the ribosyl moiety. The formation of this transition state is assisted by transient deprotonation of the 5' OH group by His 8, primed by Glu 80, which is positioned directly above the ribosyl ring oxygen by the binding of the substrate in the active site. The release of electrons towards the 1' Carbon facilitates the cleavage of the CN bond to release uracil. Protonation of the uracil moiety prior to the cleavage of the bond occurs through a water molecule activated by Arg 223, and this allows it to act as a leaving group whilst the O4 atom of the phosphate acts as a nucleophile to attack the 1' Carbon. As a result, the products are formed.
Reaction

Catalytic Sites for 1t0u

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluA8080macie:sideChainActs to modify the pKa of His 8 to allow it to act as a general acid base and deprotonate the 5'OH group of the ribosyl moiety, thus allowing formation of the oxocarbenium ion transition state.
HisA88macie:sideChainActs as a general base to deprotonate the 5'OH to allow the build up of negative charge that results in the formation of the oxocarbenium ion transition state.
ArgA223223macie:sideChainActs to allow a water molecule to act as an acid base and protonate the uracil moiety, thus allowing it to act as a leaving group.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluB8080macie:sideChainActs to modify the pKa of His 8 to allow it to act as a general acid base and deprotonate the 5'OH group of the ribosyl moiety, thus allowing formation of the oxocarbenium ion transition state.
HisB88macie:sideChainActs as a general base to deprotonate the 5'OH to allow the build up of negative charge that results in the formation of the oxocarbenium ion transition state.
ArgB223223macie:sideChainActs to allow a water molecule to act as an acid base and protonate the uracil moiety, thus allowing it to act as a leaving group.

Literature References

Notes:
Caradoc-Davies TT
Crystal structures of Escherichia coli uridine phosphorylase in two native and three complexed forms reveal basis of substrate specificity, induced conformational changes and influence of potassium.
J Mol Biol 2004 337 337-354
PubMed: 15003451
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