Crystal structure of pectin methylesterase in complex with hexasaccharide VII

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

Starting Model: experimental
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Molecular basis of the activity of the phytopathogen pectin methylesterase.

Fries, M.Ihrig, J.Brocklehurst, K.Shevchik, V.E.Pickersgill, R.W.

(2007) EMBO J 26: 3879-3887

  • DOI: https://doi.org/10.1038/sj.emboj.7601816
  • Primary Citation of Related Structures:  
    2NSP, 2NST, 2NT6, 2NT9, 2NTB, 2NTP, 2NTQ

  • PubMed Abstract: 

    We provide a mechanism for the activity of pectin methylesterase (PME), the enzyme that catalyses the essential first step in bacterial invasion of plant tissues. The complexes formed in the crystal using specifically methylated pectins, together with kinetic measurements of directed mutants, provide clear insights at atomic resolution into the specificity and the processive action of the Erwinia chrysanthemi enzyme. Product complexes provide additional snapshots along the reaction coordinate. We previously revealed that PME is a novel aspartic-esterase possessing parallel beta-helix architecture and now show that the two conserved aspartates are the nucleophile and general acid-base in the mechanism, respectively. Other conserved residues at the catalytic centre are shown to be essential for substrate binding or transition state stabilisation. The preferential binding of methylated sugar residues upstream of the catalytic site, and demethylated residues downstream, drives the enzyme along the pectin molecule and accounts for the sequential pattern of demethylation produced by both bacterial and plant PMEs.

  • Organizational Affiliation

    School of Biological and Chemical Sciences, Queen Mary, University of London, London, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pectinesterase A
A, B
342Dickeya dadantii 3937Mutation(s): 0 
Gene Names: pemApem
Find proteins for P0C1A9 (Dickeya dadantii (strain 3937))
Explore P0C1A9 
Go to UniProtKB:  P0C1A9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C1A9
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
methyl alpha-D-galactopyranuronate-(1-4)-methyl alpha-D-galactopyranuronate-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid
C, D
Glycosylation Resources
GlyTouCan:  G29545DQ
GlyCosmos:  G29545DQ
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.193α = 90
b = 85.018β = 93.43
c = 97.514γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 2.0: 2020-05-13
    Changes: Atomic model, Data collection, Derived calculations
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary