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Search The CSA
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Catalytic Site Atlas

CSA LITERATURE entry for 1k0w

E.C. nameL-ribulose-5-phosphate 4-epimerase
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) 5.1.3.4
CSA Homologues of 1k0wThere are 39 Homologs
CSA Entries With UniProtID P08203
CSA Entries With EC Number 5.1.3.4
PDBe Entry 1k0w
PDBSum Entry 1k0w
MACiE Entry M0273

Literature Report

IntroductionL-ribulose-5-phosphate-4-epimerase catalyses the interconversion of L-ribulose 5-phosphate(L-Ru5P) and D-xylulose 5-phosphate(D-Xu5P). It belongs to a superfamily of epimerases/aldolases that catalyse carbon-carbon bond cleavage reactions via a metal stabilised enolate intermediate.
The conversion from L-Ru5P to D-Xu5P allows bacteria to utilise arabinose as an energy source by converting it into an intermediate in the pentose phosphate pathway(D-Xu5P).
MechansimThe mechanism involves the initial retroaldol cleavage between C3 and C4 of the substrate after the deprotonation of the C4-OH group by a base. The cleavage generates glycolaldehyde phosphate and metal -bound enolate of dihydroxyactone as intermediates. A subsequent aldol addition of the same face of the enolate to the opposite face of the aldehyde generates the epimeric product. Tyr229 acts as the base for the deprotonation of L-Ru5P while Asp120 acts as the acid to protonate the product to complete the epimerisation. In the reverse reaction, Asp acts as the base to deprotonate D-Xu5P and Tyr229 the acid. Zn2+ acts as an electrophilic catalyst by coordinating to the ketone oxygen at C2 to promote enolate formation.
Reaction

Catalytic Sites for 1k0w

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AsnA120120macie:sideChainIn the conversion from D-Xu5P to L-Ru5P, it acts as a base to deprotonate the substrate, D-Xu5P. In the reverse reaction, it acts as an acid to protonate the product, D-Xu5P.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AsnB120120macie:sideChainIn the conversion from D-Xu5P to L-Ru5P, it acts as a base to deprotonate the substrate, D-Xu5P. In the reverse reaction, it acts as an acid to protonate the product, D-Xu5P.

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AsnC120120macie:sideChainIn the conversion from D-Xu5P to L-Ru5P, it acts as a base to deprotonate the substrate, D-Xu5P. In the reverse reaction, it acts as an acid to protonate the product, D-Xu5P.

Annotated By Reference To The Literature - Site 4 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AsnD120120macie:sideChainIn the conversion from D-Xu5P to L-Ru5P, it acts as a base to deprotonate the substrate, D-Xu5P. In the reverse reaction, it acts as an acid to protonate the product, D-Xu5P.

Annotated By Reference To The Literature - Site 5 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AsnE120120macie:sideChainIn the conversion from D-Xu5P to L-Ru5P, it acts as a base to deprotonate the substrate, D-Xu5P. In the reverse reaction, it acts as an acid to protonate the product, D-Xu5P.

Annotated By Reference To The Literature - Site 6 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AsnF120120macie:sideChainIn the conversion from D-Xu5P to L-Ru5P, it acts as a base to deprotonate the substrate, D-Xu5P. In the reverse reaction, it acts as an acid to protonate the product, D-Xu5P.

Literature References

Notes:The last eight C-terminal residues(224-231) could not be located in the structure, yet it is suggested that the tail is directed across the active site of an adjacent subunit, so the catalytic residue Tyr229 cannot be found in the pdb file. Tyr229, supported by site mutagenesis, its position and it as a conserved residue, plays a role as acid/base in catalysis. In the conversion from L-Ru5P to D-Xu5P, it acts as a base to deprotonate the substrate, L-Ru5P. In the reverse reaction, it acts as an acid to protonate the product, L-Ru5P.
Luo Y
The structure of L-ribulose-5-phosphate 4-epimerase: an aldolase-like platform for epimerization.
Biochemistry 2001 40 14763-14771
PubMed: 11732895
Lee LV
Role of metal ions in the reaction catalyzed by L-ribulose-5-phosphate 4-epimerase.
Biochemistry 2000 39 4821-4830
PubMed: 10769139
Samuel J
Catalysis and binding in L-ribulose-5-phosphate 4-epimerase: a comparison with L-fuculose-1-phosphate aldolase.
Biochemistry 2001 40 14772-14780
PubMed: 11732896
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