2EWE

Crystal structure of Pectate Lyase C R218K mutant in complex with pentagalacturonic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.186 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Structure of a Plant Cell Wall Fragment Complexed to Pectate Lyase C

Scavetta, R.D.Herron, S.R.Hotchkiss, A.T.Kita, N.Keen, N.T.Benen, J.A.Kester, H.C.Visser, J.Jurnak, F.

(1999) Plant Cell 11: 1081-1092

  • DOI: https://doi.org/10.1105/tpc.11.6.1081
  • Primary Citation of Related Structures:  
    2EWE

  • PubMed Abstract: 

    The three-dimensional structure of a complex between the pectate lyase C (PelC) R218K mutant and a plant cell wall fragment has been determined by x-ray diffraction techniques to a resolution of 2.2 A and refined to a crystallographic R factor of 18.6%. The oligosaccharide substrate, alpha-D-GalpA-([1-->4]-alpha-D-GalpA)3-(1-->4)-D-GalpA , is composed of five galacturonopyranose units (D-GalpA) linked by alpha-(1-->4) glycosidic bonds. PelC is secreted by the plant pathogen Erwinia chrysanthemi and degrades the pectate component of plant cell walls in soft rot diseases. The substrate has been trapped in crystals by using the inactive R218K mutant. Four of the five saccharide units of the substrate are well ordered and represent an atomic view of the pectate component in plant cell walls. The conformation of the pectate fragment is a mix of 21 and 31 right-handed helices. The substrate binds in a cleft, interacting primarily with positively charged groups: either lysine or arginine amino acids on PelC or the four Ca2+ ions found in the complex. The observed protein-oligosaccharide interactions provide a functional explanation for many of the invariant and conserved amino acids in the pectate lyase family of proteins. Because the R218K PelC-galacturonopentaose complex represents an intermediate in the reaction pathway, the structure also reveals important details regarding the enzymatic mechanism. Notably, the results suggest that an arginine, which is invariant in the pectate lyase superfamily, is the amino acid that initiates proton abstraction during the beta elimination cleavage of polygalacturonic acid.


  • Organizational Affiliation

    Department of Physiology and Biophysics, 346-D Med Sci I, University of California, Irvine, California 92697-4560, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pectate lyase C353Dickeya chrysanthemiMutation(s): 1 
Gene Names: pelC
EC: 4.2.2.2
UniProt
Find proteins for P11073 (Dickeya chrysanthemi)
Explore P11073 
Go to UniProtKB:  P11073
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11073
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid
B
4N/A
Glycosylation Resources
GlyTouCan:  G38578RB
GlyCosmos:  G38578RB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.14α = 90
b = 78.32β = 90
c = 94.43γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-10-20
    Changes: Database references, Structure summary
  • Version 2.2: 2023-08-23
    Changes: Data collection, Refinement description