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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1tz3
Original Entry
Title:
Transferase
Compound:
Putative sugar kinase
Mutant:
No
UniProt/Swiss-Prot:
Q8ZKR2-Q8ZKR2
EC Class:
3.6.1.26
Other CSA Entries:
Overview of all sites for 1tz3
Homologues of 1tz3
Entries for UniProt/Swiss-Prot: Q8ZKR2
Entries for EC: 3.6.1.26
Other Databases:
PDB entry: 1tz3
PDBsum entry: 1tz3
UniProt/Swiss-Prot: Q8ZKR2
IntEnz entry: 3.6.1.26
Literature Report:
Introduction:
5-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.
Mechanism:
The 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.

Sites:

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Found by:
Literature reference 
PsiBLAST alignment on 1rk2

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLYA 249 249Backbone amide
ElectrostaticTransition state
The main chain amide of Gly 249 acts as an anion hole to stabilise charge build-up in the transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 15458630 Current protein Conservation of residue
PubMed ID 15458630 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 15458630 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ALAA 250 250Backbone amide
ElectrostaticTransition state
The main chain amide of Ala 250 acts as an anion hole to stabilise charge build-up in the transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 15458630 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 15458630 Current protein Structural similarity to homologue of known mechanism
PubMed ID 15458630 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLYA 251 251Backbone amide
ElectrostaticTransition state
The main chain amide of Gly 251 acts as an anion hole to stabilise charge build-up in the transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 15458630 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 15458630 Current protein Structural similarity to homologue of known mechanism
PubMed ID 15458630 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 252 252Sidechain, Backbone amide
Acid/baseSubstrate
ElectrostaticTransition state
The 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.
Evidence from paper Evidence concerns Evidence type
PubMed ID 15458630 Current protein Structural similarity to homologue of known mechanism
PubMed ID 15458630 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 15458630 Current protein Conservation of residue
Notes:
AIR is not considered to be the physiologically relevant substrate, due to low levels of AIR in the Salmonella enterica environment.
References:
1
Crystal structure of an aminoimidazole riboside kinase from Salmonella enterica: implications for the evolution of the ribokinase superfamily.
Y. Zhang and M. Dougherty and D. M. Downs and S. E. Ealick
Structure 12, (10) 1809-21, (2004).
15458630
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