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Catalytic Site Atlas

CSA LITERATURE entry for 1idj

E.C. namepectin lyase
SpeciesAspergillus niger (strain CBS 513.88 / FGSC A1513)
E.C. Number (IntEnz)
CSA Homologues of 1idj1bn8,1idk,1qcx,2bsp,2qx3,2qxz,2qy1,
CSA Entries With UniProtID Q01172
CSA Entries With EC Number
PDBe Entry 1idj
PDBSum Entry 1idj
MACiE Entry 1idj

Literature Report

IntroductionPectin lyases are enzymes that catalyse the degradation of pectin, a main structural polysaccharide of the primary cell wall and middle lamella of higher plants. Pectin is a methylesteried form of polygalacturonic acid. The enzymes utilise a beta-elimination reaction to cleave the alpha-d-(1,4) glycosidic bond between galacturonosyl residues in the homogalacturonan (the so-called `smooth') part of the pectin molecule, resulting in the formation of a C4-C5 double bond at the non-reducing end of the cleaved polysaccharide. Pectin lyases belong to the family of polysaccharide lyases of which currently 12 families are known. In addition to the role of pectin lyase in microbial phytopathogenesis, this enzyme has biotechnological potential in fruit juice industries due to the fact that it degrades pectin without disturbing the ester group which is responsible for specific aroma of the juice and also it does not lead to methanol formation which is toxic. This enzyme has potential applications also in textile industries, in degumming and retting of natural fibers like ramie, hemp, jute, flax, etc.
MechansimArg236 is the catalytic base that initiates the beta-elimination reaction on pectin polymers which results in the formation of 4,5-unsaturated oligogalacturonides.

Catalytic Sites for 1idj

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ArgA236256macie:sideChainDeprotonates pectin polymer to cleave the alpha-d-(1,4)-glycosidic bond.
LysA239259macie:sideChainLys239 acts to lower the pKa of the guanidinium group of Arg236, in order to increase its basicity. Lys239 remains charged as a result of bulk solvent accessibility.
ArgA176196macie:sideChainArg176 functions to lower the pKa of the guanidinium group of Arg236, in order to make it more basic.
AspA154174macie:sideChainrg176 is maintained in a protonated state by the neighbouring Asp154 electrostatically.

Literature References

Sánchez-Torres P
Identification of amino acid residues critical for catalysis and stability in Aspergillus niger family 1 pectin lyase A.
Biochem J 2003 370 331-337
PubMed: 12418964