2NST

Crystal structure of pectin methylesterase D178A mutant in complex with hexasaccharide II

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

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: 10.1038/sj.emboj.7601816
  • Primary Citation of Related Structures:  

  • 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 wit ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pectinesterase A
A, B
342Dickeya dadantii (strain 3937)Mutation(s): 1 
Gene Names: pemA (pem)
EC: 3.1.1.11
Find proteins for P0C1A9 (Dickeya dadantii (strain 3937))
Go to UniProtKB:  P0C1A9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M8C
Query on M8C
Download SDF File 
Download CCD File 
C, D
METHYL ALPHA-D-GALACTOPYRANURONATE
ALPHA-D-GALACTOPYRANURONIC METHYL ESTER; (2S,3R,4S,5R,6S)-METHYL 3,4,5,6-TETRAHYDROXY-TETRAHYDRO-2H-PYRAN-2-CARBOXYLATE
C7 H12 O7
DICCNWCUKCYGNF-KGJVWPDLSA-N
 Ligand Interaction
ADA
Query on ADA
Download SDF File 
Download CCD File 
C, D
ALPHA-D-GALACTOPYRANURONIC ACID
ALPHA D-GALACTURONIC ACID
C6 H10 O7
AEMOLEFTQBMNLQ-BKBMJHBISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.012α = 90.00
b = 84.840β = 93.57
c = 97.163γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
REFMACphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance