Pectin lyase A (polysaccharide lyase 1 family)

 

Pectin 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.

 

Reference Protein and Structure

Sequence
Q01172 UniProt (4.2.2.10) IPR012334 (Sequence Homologues) (PDB Homologues)
Biological species
Aspergillus niger (Fungus) Uniprot
PDB
1idj - PECTIN LYASE A (2.4 Å) PDBe PDBsum 1idj
Catalytic CATH Domains
2.160.20.10 CATHdb (see all for 1idj)
Click To Show Structure

Enzyme Reaction (EC:4.2.2.10)

apiogalacteronin
CHEBI:60176ChEBI
→
4-Deoxy-alpha-L-erythro-hex-4-enopyranuronoside
CHEBI:1822ChEBI
+
D-galactopyranuronic acid
CHEBI:4153ChEBI
Alternative enzyme names: PL, PMGL, PNL, Endo-pectin lyase, Pectin trans-eliminase, Pectin methyltranseliminase, Pectolyase, Polymethylgalacturonic transeliminase,

Enzyme Mechanism

Introduction

Arg236 is the catalytic base that initiates the beta-elimination reaction on pectin polymers which results in the formation of 4,5-unsaturated oligogalacturonides.

Catalytic Residues Roles

UniProt PDB* (1idj)
Lys259 Lys239A Lys239 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. electrostatic stabiliser
Asp174 Asp154A rg176 is maintained in a protonated state by the neighbouring Asp154 electrostatically. electrostatic stabiliser
Arg196 Arg176A Arg176 functions to lower the pKa of the guanidinium group of Arg236, in order to make it more basic. electrostatic stabiliser
Arg256 Arg236A Deprotonates pectin polymer to cleave the alpha-d-(1,4)-glycosidic bond. proton shuttle (general acid/base)
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

References

  1. Sánchez-Torres P et al. (2003), Biochem J, 370, 331-337. Identification of amino acid residues critical for catalysis and stability in Aspergillus niger family 1 pectin lyase A. DOI:10.1042/bj20021071. PMID:12418964.
  2. Charnock SJ et al. (2002), Proc Natl Acad Sci U S A, 99, 12067-12072. Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases. DOI:10.1073/pnas.182431199. PMID:12221284.

Step 1.

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Catalytic Residues Roles

Residue Roles
Arg236A proton shuttle (general acid/base)
Lys239A electrostatic stabiliser
Arg176A electrostatic stabiliser
Asp154A electrostatic stabiliser

Chemical Components

Step 1.

Contributors

Anna Waters, Craig Porter, Gemma L. Holliday, James Willey