The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi.
The "family 9 polysaccharide lyase" pectate lyase L (Pel9A) from Erwinia chrysanthemi comprises a 10-coil parallel beta-helix domain with distinct structural features including an asparagine ladder and aromatic stack at novel positions within the superhelical structure. Pel9A has a single high affinity calcium-binding site strikingly similar to the "primary" calcium-binding site described previously for the family Pel1A pectate lyases, and there is strong evidence for a common second calcium ion that binds between enzyme and substrate in the "Michaelis" complex. Although the primary calcium ion binds substrate in subsite -1, it is the second calcium ion, whose binding site is formed by the coming together of enzyme and substrate, that facilitates abstraction of the C5 proton from the sacharride in subsite +1. The role of the second calcium is to withdraw electrons from the C6 carboxylate of the substrate, thereby acidifying the C5 proton facilitating its abstraction and resulting in an E1cb-like anti-beta-elimination mechanism. The active site geometries and mechanism of Pel1A and Pel9A are closely similar, but the catalytic base is a lysine in the Pel9A enzymes as opposed to an arginine in the Pel1A enzymes.
Jenkins
John
J
Institute of Food Research, Norwich Research Park, Colney Lane, Norwich, NR4 7UA, United Kingdom.
Shevchik
Vladimir E
VE
Hugouvieux-Cotte-Pattat
Nicole
N
Pickersgill
Richard W
RW
D016974:Dickeya chrysanthemi / Q000737:chemistry / Q000201:enzymology*; D008958:Models, Molecular; D011133:Polysaccharide-Lyases / Q000737:chemistry*; D011487:Protein Conformation; D017434:Protein Structure, Tertiary
D011133:Polysaccharide-Lyases; C023911:pectate lyase