Crystal structure of pectate lyase Pel9A

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.177 

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The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi

Jenkins, J.Shevchik, V.E.Hugouvieux-Cotte-Pattat, N.Pickersgill, R.W.

(2004) J Biol Chem 279: 9139-9145

  • DOI: https://doi.org/10.1074/jbc.M311390200
  • Primary Citation of Related Structures:  

  • 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.

  • Organizational Affiliation

    Institute of Food Research, Norwich Research Park, Colney Lane, Norwich, NR4 7UA, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pectate lyase400Dickeya chrysanthemiMutation(s): 0 
Gene Names: PelL
Find proteins for P0C1A7 (Dickeya dadantii (strain 3937))
Explore P0C1A7 
Go to UniProtKB:  P0C1A7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C1A7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.33α = 90
b = 57.83β = 90
c = 114.93γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
ARP/wARPmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance