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Catalytic Site Atlas

CSA LITERATURE entry for 1tz3

E.C. nameCDP-diacylglycerol diphosphatase
SpeciesSalmonella typhimurium lt2 ()
E.C. Number (IntEnz) 3.6.1.26
CSA Homologues of 1tz3There are 100 Homologs
CSA Entries With UniProtID
CSA Entries With EC Number 3.6.1.26
PDBe Entry 1tz3
PDBSum Entry 1tz3
MACiE Entry 1tz3

Literature Report

Introduction5-aminoimidazole ribotide (AIR) is a branch point metabolite in the biosynthetic pathways of purines and thiamin. Although AIR cannot be efficiently taken up by most bacteria, 5-aminoimidazole riboside (AIRs) can. Aminoimidazole riboside kinase catalyses the phosphorylation of AIRs into AIR to feed into purine and thiamin biosynthesis pathways.
MechansimThe mechanism proposed is mainly by homology to other ribokinases, such as human adenosine kinase.
Asp 252 is a general base and deprotonates the 5' hydroxyl group of the ribose.
The deprotonated hydroxyl attacks the gamma-phosphate of ATP in an inline displacement mechanism.
The backbone amides of Gly 249, Ala 250, Gly 251 and Asp 252 act as an anion hole to stabilise negative charge build-up in the pentacovalent transition state.
The products are AIR and ADP.
Reaction

Catalytic Sites for 1tz3

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GlyA249249macie:mainChainAmideThe main chain amide of Gly 249 acts as an anion hole to stabilise charge build-up in the transition state.
GlyA251251macie:mainChainAmideThe main chain amide of Gly 251 acts as an anion hole to stabilise charge build-up in the transition state.
AspA252252macie:sideChainThe side chain of Asp 252 deprotonates the 5' hydroxyl of the substrate, making it more nucleophilic.
The main chain amide acts as an anion hole to stabilise charge build-up in the transition state.
AspA252252macie:mainChainAmideThe side chain of Asp 252 deprotonates the 5' hydroxyl of the substrate, making it more nucleophilic.
The main chain amide acts as an anion hole to stabilise charge build-up in the transition state.
AlaA250250macie:mainChainAmideThe main chain amide of Ala 250 acts as an anion hole to stabilise charge build-up in the transition state.

Annotated By Reference To The Literature - Site 4 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GlyB249249macie:mainChainAmideThe main chain amide of Gly 249 acts as an anion hole to stabilise charge build-up in the transition state.
GlyB251251macie:mainChainAmideThe main chain amide of Gly 251 acts as an anion hole to stabilise charge build-up in the transition state.
AspB252252macie:sideChainThe side chain of Asp 252 deprotonates the 5' hydroxyl of the substrate, making it more nucleophilic.
The main chain amide acts as an anion hole to stabilise charge build-up in the transition state.
AspB252252macie:mainChainAmideThe side chain of Asp 252 deprotonates the 5' hydroxyl of the substrate, making it more nucleophilic.
The main chain amide acts as an anion hole to stabilise charge build-up in the transition state.
AlaB250250macie:mainChainAmideThe main chain amide of Ala 250 acts as an anion hole to stabilise charge build-up in the transition state.

Literature References

Notes:AIR is not considered to be the physiologically relevant substrate, due to low levels of AIR in the Salmonella enterica environment.
Zhang Y
Crystal structure of an aminoimidazole riboside kinase from Salmonella enterica: implications for the evolution of the ribokinase superfamily.
Structure 2004 12 1809-1821
PubMed: 15458630
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