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Catalytic Site Atlas

CSA LITERATURE entry for 1nn4

E.C. nameribose-5-phosphate isomerase
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) 5.3.1.6
CSA Homologues of 1nn41o1x,2vvr,3he8,3hee,
CSA Entries With UniProtID P37351
CSA Entries With EC Number 5.3.1.6
PDBe Entry 1nn4
PDBSum Entry 1nn4
MACiE Entry 1nn4

Literature Report

IntroductionRibose-5-phosphate isomerase is able to catalyse the interconversion of Ribose-5-phosphate and Ribulose-5-phosphate, an isomerisation reaction involving the open chain forms of the two sugars, important in the pentose phosphate pathway. In E. coli there are two forms of the enzyme, which although they catalyse the same reaction, have entirely different mechanisms and catalytic residues. The less common E.coli RpiB is described here.
MechansimThe overall mechanism of the reaction is through concerted acid-base catalysis, similar to that employed by Triose Phosphate Isomerase. Initial deprotonation of the C2 atom of Ribose-5-phosphate by the catalytic base Cys 66 primed by Asp 9 leads to the formation of an enediolate intermediate, stabilised by Arg 137. Protonation of the C1's oxygen by His 10, coupled to reprotonation of the 1C by the Cys 66 residue leads to the collapse of this intermediate, forming Ribulose-5-phosphate in the open ring form.
Reaction

Catalytic Sites for 1nn4

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisA1010macie:sideChainActs as acid to protonate the enediolate intermediate thus facilitating its collapse.
ArgA137137macie:sideChainStabilises the enediolate intermediate through electrostatic interaction between the negatively charged oxygen on the intermediate and the positively charged lysine.
CysA6666macie:sideChainActs as the general base in the abstraction of a proton from Ribose-5-phosphate, then protonates the intermediate to facilitate its collapse.
AspA99macie:sideChainActs to stabilise the catalytically active form of Cys 66 as part of an Asp Cys diad. This assists in the deprotonation of the substrate to form the enediolate intermediate.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisB1010macie:sideChainActs as acid to protonate the enediolate intermediate thus facilitating its collapse.
ArgB137137macie:sideChainStabilises the enediolate intermediate through electrostatic interaction between the negatively charged oxygen on the intermediate and the positively charged lysine.
CysB6666macie:sideChainActs as the general base in the abstraction of a proton from Ribose-5-phosphate, then protonates the intermediate to facilitate its collapse.
AspB99macie:sideChainActs to stabilise the catalytically active form of Cys 66 as part of an Asp Cys diad. This assists in the deprotonation of the substrate to form the enediolate intermediate.

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisC1010macie:sideChainActs as acid to protonate the enediolate intermediate thus facilitating its collapse.
ArgC137137macie:sideChainStabilises the enediolate intermediate through electrostatic interaction between the negatively charged oxygen on the intermediate and the positively charged lysine.
CysC6666macie:sideChainActs as the general base in the abstraction of a proton from Ribose-5-phosphate, then protonates the intermediate to facilitate its collapse.
AspC99macie:sideChainActs to stabilise the catalytically active form of Cys 66 as part of an Asp Cys diad. This assists in the deprotonation of the substrate to form the enediolate intermediate.

Annotated By Reference To The Literature - Site 4 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisD1010macie:sideChainActs as acid to protonate the enediolate intermediate thus facilitating its collapse.
ArgD137137macie:sideChainStabilises the enediolate intermediate through electrostatic interaction between the negatively charged oxygen on the intermediate and the positively charged lysine.
CysD6666macie:sideChainActs as the general base in the abstraction of a proton from Ribose-5-phosphate, then protonates the intermediate to facilitate its collapse.
AspD99macie:sideChainActs to stabilise the catalytically active form of Cys 66 as part of an Asp Cys diad. This assists in the deprotonation of the substrate to form the enediolate intermediate.

Literature References

Notes:
Zhang RG
The 2.2 A resolution structure of RpiB/AlsB from Escherichia coli illustrates a new approach to the ribose-5-phosphate isomerase reaction.
J Mol Biol 2003 332 1083-1094
PubMed: 14499611
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