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Catalytic Site Atlas

CSA LITERATURE entry for 1rk2

E.C. nameribokinase
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) 2.7.1.15
CSA Homologues of 1rk2There are 67 Homologs
CSA Entries With UniProtID P0A9J6
CSA Entries With EC Number 2.7.1.15
PDBe Entry 1rk2
PDBSum Entry 1rk2
MACiE Entry 1rk2

Literature Report

IntroductionRibokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. The reaction is the first step in ribose metabolism and acts partly to trap ribose within the cell after uptake. Phosphorylation also prepares the sugar for use in the synthesis of nucleotides and histidine and for entry into the pentose phosphate pathway.
MechansimAsp255 acts as a base to deprotonate the O5'-hydroxyl group of ribose. The negatively charged O5' atom then makes a direct nucleophilic attack on the gamma-phosphate group of ATP in an in-line mechanism. An anion hole formed by backbone amide group of residues 252-255(Ala252,Ala253,Gly254,Asp255) stabilise the transition state.
Reaction

Catalytic Sites for 1rk2

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GlyA254254macie:mainChainAmideIt forms an oxyanion hole to stabilise the transition state.
AspA255255macie:sideChainIts side chain acts as a base to deprotonate the O5'-hydroxyl group of ribose to promote its nucleophilic attack to gamma-phosphate group of ATP. Its backbone amide forms an oxyanion hole to stabilise the transition state.
AlaA253253macie:mainChainAmideIt forms an oxyanion hole to stabilise the transition state.
AlaA252252macie:mainChainAmideIt forms an oxyanion hole to stabilise the transition state.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GlyB254254macie:mainChainAmideIt forms an oxyanion hole to stabilise the transition state.
AspB255255macie:sideChainIts side chain acts as a base to deprotonate the O5'-hydroxyl group of ribose to promote its nucleophilic attack to gamma-phosphate group of ATP. Its backbone amide forms an oxyanion hole to stabilise the transition state.
AlaB253253macie:mainChainAmideIt forms an oxyanion hole to stabilise the transition state.
AlaB252252macie:mainChainAmideIt forms an oxyanion hole to stabilise the transition state.

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GlyC254254macie:mainChainAmideIt forms an oxyanion hole to stabilise the transition state.
AspC255255macie:sideChainIts side chain acts as a base to deprotonate the O5'-hydroxyl group of ribose to promote its nucleophilic attack to gamma-phosphate group of ATP. Its backbone amide forms an oxyanion hole to stabilise the transition state.
AlaC253253macie:mainChainAmideIt forms an oxyanion hole to stabilise the transition state.
AlaC252252macie:mainChainAmideIt forms an oxyanion hole to stabilise the transition state.

Annotated By Reference To The Literature - Site 4 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GlyD254254macie:mainChainAmideIt forms an oxyanion hole to stabilise the transition state.
AspD255255macie:sideChainIts side chain acts as a base to deprotonate the O5'-hydroxyl group of ribose to promote its nucleophilic attack to gamma-phosphate group of ATP. Its backbone amide forms an oxyanion hole to stabilise the transition state.
AlaD253253macie:mainChainAmideIt forms an oxyanion hole to stabilise the transition state.
AlaD252252macie:mainChainAmideIt forms an oxyanion hole to stabilise the transition state.

Literature References

Notes:
Sigrell JA
Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8 A resolution: insights into a new family of kinase structures.
Structure 1998 6 183-193
PubMed: 9519409
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