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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1rk2
Original Entry
Title:
Transferase
Compound:
Ribokinase
Mutant:
No
UniProt/Swiss-Prot:
P05054-RBSK_ECOLI
EC Class:
2.7.1.15
Other CSA Entries:
Overview of all sites for 1rk2
Homologues of 1rk2
Entries for UniProt/Swiss-Prot: P05054
Entries for EC: 2.7.1.15
Other Databases:
PDB entry: 1rk2
PDBsum entry: 1rk2
UniProt/Swiss-Prot: P05054
IntEnz entry: 2.7.1.15
Literature Report:
Introduction:
Ribokinase 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.
Mechanism:
Asp255 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.
Sites:

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Found by:
Literature reference 
PsiBLAST alignment on 1tz3

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ALAA 252 252Backbone amide
ElectrostaticTransition state
It forms an oxyanion hole to stabilise the transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 9519409 Current protein Structural similarity to homologue of known mechanism
PubMed ID 9519409 Current protein Residue is positioned appropriately
PubMed ID 9519409 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ALAA 253 253Backbone amide
ElectrostaticTransition state
It forms an oxyanion hole to stabilise the transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 9519409 Current protein Structural similarity to homologue of known mechanism
PubMed ID 9519409 Current protein Conservation of residue
PubMed ID 9519409 Current protein Residue is positioned appropriately

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLYA 254 254Backbone amide
ElectrostaticTransition state
It forms an oxyanion hole to stabilise the transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 9519409 Current protein Residue is positioned appropriately
PubMed ID 9519409 Current protein Structural similarity to homologue of known mechanism
PubMed ID 9519409 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 255 255Sidechain
Acid/baseSubstrate
ElectrostaticTransition state
Its 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.
Evidence from paper Evidence concerns Evidence type
PubMed ID 9519409 Current protein Conservation of residue
PubMed ID 9519409 Current protein Structural similarity to homologue of known mechanism
PubMed ID 9519409 Current protein Residue is positioned appropriately (ligand position known)
References:
1
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.
J. A. Sigrell and A. D. Cameron and T. A. Jones and S. L. Mowbray
Structure 6, (2) 183-93, (1998).
9519409
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