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 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.4 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
  • Primary Citation of Related Structures:  
    1QJV

  • 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 triad, and in some enzymes the role of the aspartate residue is replaced by a main-chain carbonyl oxygen atom ...

    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: 
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PECTIN METHYLESTERASEA, B342Dickeya chrysanthemiMutation(s): 1 
Gene Names: pemApem
EC: 3.1.1.11
UniProt
Find proteins for P0C1A8 (Dickeya chrysanthemi)
Explore P0C1A8 
Go to UniProtKB:  P0C1A8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C1A8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth 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 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.694α = 90
b = 85.507β = 93.69
c = 96.69γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-07-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-07-24
    Changes: Data collection