1XG2

Crystal structure of the complex between pectin methylesterase and its inhibitor protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for the Interaction between Pectin Methylesterase and a Specific Inhibitor Protein

Di Matteo, A.Giovane, A.Raiola, A.Camardella, L.Bonivento, D.De Lorenzo, G.Cervone, F.Bellincampi, D.Tsernoglou, D.

(2005) Plant Cell 17: 849-858

  • DOI: 10.1105/tpc.104.028886
  • Primary Citation of Related Structures:  
    1XG2

  • PubMed Abstract: 
  • Pectin, one of the main components of the plant cell wall, is secreted in a highly methyl-esterified form and subsequently deesterified in muro by pectin methylesterases (PMEs). In many developmental processes, PMEs are regulated by either differential expression or posttranslational control by protein inhibitors (PMEIs) ...

    Pectin, one of the main components of the plant cell wall, is secreted in a highly methyl-esterified form and subsequently deesterified in muro by pectin methylesterases (PMEs). In many developmental processes, PMEs are regulated by either differential expression or posttranslational control by protein inhibitors (PMEIs). PMEIs are typically active against plant PMEs and ineffective against microbial enzymes. Here, we describe the three-dimensional structure of the complex between the most abundant PME isoform from tomato fruit (Lycopersicon esculentum) and PMEI from kiwi (Actinidia deliciosa) at 1.9-A resolution. The enzyme folds into a right-handed parallel beta-helical structure typical of pectic enzymes. The inhibitor is almost all helical, with four long alpha-helices aligned in an antiparallel manner in a classical up-and-down four-helical bundle. The two proteins form a stoichiometric 1:1 complex in which the inhibitor covers the shallow cleft of the enzyme where the putative active site is located. The four-helix bundle of the inhibitor packs roughly perpendicular to the main axis of the parallel beta-helix of PME, and three helices of the bundle interact with the enzyme. The interaction interface displays a polar character, typical of nonobligate complexes formed by soluble proteins. The structure of the complex gives an insight into the specificity of the inhibitor toward plant PMEs and the mechanism of regulation of these enzymes.


    Related Citations: 
    • Pectin methylesterase inhibitor
      Giovane, A., Servillo, L., Balestrieri, C., Raiola, A., D'Avino, R., Tamburrini, M., Ciardiello, M.A., Camardella, L.
      (2004) Biochim Biophys Acta 1696: 245
    • Tomato pectin methylesterase: modeling, fluorescence, and inhibitor interaction studies-comparison with the bacterial (Erwinia chrysanthemi) enzyme
      D'Avino, R., Camardella, L., Christensen, T.M., Giovane, A., Servillo, L.
      (2003) Proteins 53: 830
    • Pectin methylesterases: cell wall enzymes with important roles in plant physiology
      Micheli, F.
      (2001) Trends Plant Sci 6: 414

    Organizational Affiliation

    Department of Biochemical Sciences, University of Rome, 00185 Rome, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pectinesterase 1 A317Solanum lycopersicumMutation(s): 0 
Gene Names: PME1.9
EC: 3.1.1.11
Find proteins for P14280 (Solanum lycopersicum)
Explore P14280 
Go to UniProtKB:  P14280
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pectinesterase inhibitor B153Actinidia chinensisMutation(s): 0 
Find proteins for P83326 (Actinidia deliciosa)
Explore P83326 
Go to UniProtKB:  P83326
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.379α = 90
b = 90.379β = 90
c = 149.095γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance