1QJV

Pectin methylesterase PemA from Erwinia chrysanthemi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Three-Dimensional Structure of Erwinia Chrysanthemi Pectin Methylesterase Reveals a Novel Esterase Active Site

Jenkins, J.Mayans, O.Smith, D.Worboys, K.Pickersgill, R.

(2001) J.Mol.Biol. 305: 951

  • DOI: 10.1006/jmbi.2000.4324

  • PubMed Abstract: 
  • Most structures of neutral lipases and esterases have been found to adopt the common alpha/beta hydrolase fold and contain a catalytic Ser-His-Asp triad. Some variation occurs in both the overall protein fold and in the location of the catalytic tria ...

    Most structures of neutral lipases and esterases have been found to adopt the common alpha/beta hydrolase fold and contain a catalytic Ser-His-Asp triad. Some variation occurs in both the overall protein fold and in the location of the catalytic triad, and in some enzymes the role of the aspartate residue is replaced by a main-chain carbonyl oxygen atom. Here, we report the crystal structure of pectin methylesterase that has neither the common alpha/beta hydrolase fold nor the common catalytic triad. The structure of the Erwinia chrysanthemi enzyme was solved by multiple isomorphous replacement and refined at 2.4 A to a conventional crystallographic R-factor of 17.9 % (R(free) 21.1 %). This is the first structure of a pectin methylesterase and reveals the enzyme to comprise a right-handed parallel beta-helix as seen in the pectinolytic enzymes pectate lyase, pectin lyase, polygalacturonase and rhamnogalacturonase, and unlike the alpha/beta hydrolase fold of rhamnogalacturonan acetylesterase with which it shares esterase activity. Pectin methylesterase has no significant sequence similarity with any protein of known structure. Sequence conservation among the pectin methylesterases has been mapped onto the structure and reveals that the active site comprises two aspartate residues and an arginine residue. These proposed catalytic residues, located on the solvent-accessible surface of the parallel beta-helix and in a cleft formed by external loops, are at a location similar to that of the active site and substrate-binding cleft of pectate lyase. The structure of pectin methylesterase is an example of a new family of esterases.


    Related Citations: 
    • Production of Pectin Methylesterase from Erwinia Chrysanthemi B374 in Bacillus Subtilis
      Heikinheimo, R.,Hemila, H.,Pakkanen, R.,Palva, I.
      (1991) Appl.Microbiol.Biotechnol. 35: 51
    • Molecular Cloning and Nucleotide Sequence of the Pectin Methyl Esterase Gene of Erwinia Chrysanthemi B374
      Plastow, G.S.
      (1988) Mol.Microbiol. 2: 247
    • Characterization and Overexpression of the Pem Gene Encoding Pectin Methylesterase from Erwinia Chrysanthemi Strain-3937
      Laurent, F.,Kotoujansky, A.,Labesse, G.,Bertheau, Y.
      (1993) Gene 131: 17


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PECTIN METHYLESTERASE
A, B
342Dickeya chrysanthemiGene Names: pemA (pem)
EC: 3.1.1.11
Find proteins for P0C1A8 (Dickeya chrysanthemi)
Go to UniProtKB:  P0C1A8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.694α = 90.00
b = 85.507β = 93.69
c = 96.690γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-07-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance