1RU4

Crystal structure of pectate lyase Pel9A

Summary for 1RU4

• Entry DOI: 10.2210/pdb1ru4/pdb
• Descriptor: Pectate lyase, CALCIUM ION (3 entities in total)
• Functional Keywords: parallel beta-helix, lyase
• Biological source: Erwinia chrysanthemi
• Total number of polymer chains: 1
• Total formula weight: 42907.47

Authors

Jenkins, J.,Shevchik, V.E.,Hugouvieux-Cotte-Pattat, N.,Pickersgill, R.W. (deposition date: 2003-12-11, release date: 2004-04-13, Last modification date: 2024-10-30)

Primary citation

Jenkins, J.,Shevchik, V.E.,Hugouvieux-Cotte-Pattat, N.,Pickersgill, R.W.
The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi
J.Biol.Chem., 279:9139-9145, 2004

PubMed Abstract: 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.

PubMed: 14670977
DOI: 10.1074/jbc.M311390200

Experimental method

X-RAY DIFFRACTION (1.6 Å)