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Catalytic Site Atlas

CSA LITERATURE entry for 1ru4

E.C. namepectate lyase
SpeciesErwinia chrysanthemi (Bacteria)
E.C. Number (IntEnz) 4.2.2.2
CSA Homologues of 1ru4
CSA Entries With UniProtID P0C1A6
CSA Entries With EC Number 4.2.2.2
PDBe Entry 1ru4
PDBSum Entry 1ru4
MACiE Entry M0184

Literature Report

IntroductionEndo-acting pectate lyase L (Pel9A) is from the bacteria Erwini chrysanthemi. It catalyses the eliminative cleavage of pectate to give oligosaccharides with 4-deoxy-alpha-D-gluc-4-enuronosyl groups at their non-reducing ends. This particular bacteria causes soft rot diseases. It secretes enzymes such as Pel9A which break down pectin, a key component of cell walls.
MechansimThis reaction is thought to occur via an E1cb mechanism. 1. Ca2+ and Asn interact with the substrate carboxylate, making the C5 proton more acidic. 2. Lys 273 acts as a base by taking the C5 proton, forming the substrate's conjugate base. 3. The carboxylate reforms and the C4-O bond is cleaved. 4. Solvent water protonates the glycosidic oxygen as it leaves.

Catalytic Sites for 1ru4

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysA273273macie:sideChainLys 273 deprotonates atom C5 of the substrate, to form the conjugate base.
AsnA268268macie:sideChainActivates the substrate by acidifying the C5 proton. It stabilises the conjugate base.

Literature References

Notes:
Jenkins J
The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi.
J Biol Chem 2004 279 9139-9145
PubMed: 14670977
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