1GXM

Family 10 polysaccharide lyase from Cellvibrio cellulosa

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Convergent Evolution Sheds Light on the Anti-Beta-Elimination Mechanism Common to Family 1 and 10 Polysaccharide Lyases

Charnock, S.J., Brown, I.E., Turkenburg, J.P., Black, G.W., Davies, G.J.

(2002) Proc Natl Acad Sci U S A 99: 12067

  • DOI: 10.1073/pnas.182431199
  • Primary Citation of Related Structures:  
    1GXM, 1GXN, 1GXO

  • PubMed Abstract: 

    • Enzyme-catalyzed beta-elimination of sugar uronic acids, exemplified by the degradation of plant cell wall pectins, plays an important role in a wide spectrum of biological processes ranging from the recycling of plant biomass through to pathogen virulence ...

    Enzyme-catalyzed beta-elimination of sugar uronic acids, exemplified by the degradation of plant cell wall pectins, plays an important role in a wide spectrum of biological processes ranging from the recycling of plant biomass through to pathogen virulence. The three-dimensional crystal structure of the catalytic module of a "family PL-10" polysaccharide lyase, Pel10Acm from Cellvibrio japonicus, solved at a resolution of 1.3 A, reveals a new polysaccharide lyase fold and is the first example of a polygalacturonic acid lyase that does not exhibit the "parallel beta-helix" topology. The "Michaelis" complex of an inactive mutant in association with the substrate trigalacturonate/Ca2+ reveals the catalytic machinery harnessed by this polygalacturonate lyase, which displays a stunning resemblance, presumably through convergent evolution, to the tetragalacturonic acid complex observed for a structurally unrelated polygalacturonate lyase from family PL-1. Common coordination of the -1 and +1 subsite saccharide carboxylate groups by a protein-liganded Ca2+ ion, the positioning of an arginine catalytic base in close proximity to the alpha-carbon hydrogen and numerous other conserved enzyme-substrate interactions, considered in light of mutagenesis data for both families, suggest a generic polysaccharide anti-beta-elimination mechanism.

    Organizational Affiliation: 

    York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, United Kingdom.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PECTATE LYASEA, B332Cellvibrio japonicusMutation(s): 0 
Gene Names: Pel10A
EC: 4.2.2.2
UniProt
Find proteins for Q9F7L3 (Cellvibrio japonicus)
Explore Q9F7L3 
Go to UniProtKB:  Q9F7L3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F7L3
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.67α = 90
b = 106.113β = 91.95
c = 55.365γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-10-04
    Type: Initial release
  • Version 1.1: 2011-10-19
    Changes: Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2019-05-22
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-05-29
    Changes: Data collection, Experimental preparation