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Search The CSA
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Catalytic Site Atlas

CSA LITERATURE entry for 1czf

E.C. namepolygalacturonase
SpeciesAspergillus niger (strain CBS 513.88 / FGSC A1513)
E.C. Number (IntEnz) 3.2.1.15
CSA Homologues of 1czfThere are 11 Homologs
CSA Entries With UniProtID P26214
CSA Entries With EC Number 3.2.1.15
PDBe Entry 1czf
PDBSum Entry 1czf
MACiE Entry 1czf

Literature Report

IntroductionPolygalacturonases hydrolyse the 1,4 linkage of de-esterified pectase. The enzyme belongs to the family 28 of glycosyl hydrolases, catalysing hydrolysis with inversion of stereochemistry at the anomeric carbon
MechansimA hydrolytic water molecule, activated through hydrogen bonding to Asp180 and Asp202 attacks the glycosidic link in a single displacement reaction. The conserved Asp201 acts as a proton donor to the departing glycosidic oxygen. His 223 participates in a proton relay with Asp180, ensuring it is deprotonated to interact with the hydrolytic water.
Reaction

Catalytic Sites for 1czf

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspA202202macie:sideChainThe residue activates the hydrolytic water molecule towards nucleophilic attack at the substrate glycosidic bond through hydrogen bonding.
AspA180180macie:sideChainThe residue acts as a general base towards the hydrolytic water molecule, activating it towards nucleophilic attack at the glycosidic bond. Interactions with a structurally aligned His223 creates a proton shuttle between the residues, ensuring that Asp202 is deprotonated in the presence of the attacking water molecule.
AspA201201macie:sideChainThe residue acts as a general acid towards the departing glycosidic oxygen.
HisA223223macie:sideChainCrystallographic data and mutagenesis studies have shown His223 to be catalytically essential to the reaction. The residue is thought to act as a proton acceptor from the hydrolytic water via a proton shuttle with Asp180.

Literature References

Notes:
van Santen Y
1.68-A crystal structure of endopolygalacturonase II from Aspergillus niger and identification of active site residues by site-directed mutagenesis.
J Biol Chem 1999 274 30474-30480
PubMed: 10521427
Cho SW
The X-ray structure of Aspergillus aculeatus polygalacturonase and a modeled structure of the polygalacturonase-octagalacturonate complex.
J Mol Biol 2001 311 863-878
PubMed: 11518536
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