1NKG

Rhamnogalacturonan lyase from Aspergillus aculeatus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


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


Literature

Rhamnogalacturonan lyase reveals a unique three-domain modular structure for polysaccharide lyase family 4.

McDonough, M.A., Kadirvelraj, R., Harris, P., Poulsen, J.C., Larsen, S.

(2004) FEBS Lett 565: 188-194

  • DOI: 10.1016/j.febslet.2004.03.094
  • Primary Citation of Related Structures:  
    1NKG

  • PubMed Abstract: 

    • Rhamnogalacturonan lyase (RG-lyase) specifically recognizes and cleaves alpha-1,4 glycosidic bonds between L-rhamnose and D-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. The three-dimensional structure of RG-lyase from Aspergillus aculeatus has been determined to 1 ...

    Rhamnogalacturonan lyase (RG-lyase) specifically recognizes and cleaves alpha-1,4 glycosidic bonds between L-rhamnose and D-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. The three-dimensional structure of RG-lyase from Aspergillus aculeatus has been determined to 1.5 A resolution representing the first known structure from polysaccharide lyase family 4 and of an enzyme with this catalytic specificity. The 508-amino acid polypeptide displays a unique arrangement of three distinct modular domains. Each domain shows structural homology to non-catalytic domains from other carbohydrate active enzymes.

    Related Citations: 
    • A stepwise optimization of crystals of rhamnogalacturonan lyase from Aspergillus aculeatus
      Kadirvelraj, R., Harris, P., Poulsen, J.-C.N., Kauppinen, S., Larsen, S.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 1346
    Organizational Affiliation: 

    Centre for Crystallographic Studies, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, DK, Denmark. michael.mcdonough@chemistry.oxford.ac.uk



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Rhamnogalacturonase BA508Aspergillus aculeatusMutation(s): 0 
Gene Names: RHGB, rglA, RGL4
EC: 4.2.2 (PDB Primary Data), 4.2.2.23 (UniProt)
UniProt
Find proteins for Q00019 (Aspergillus aculeatus)
Explore Q00019 
Go to UniProtKB:  Q00019
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00019
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.009α = 90
b = 77.009β = 90
c = 170.787γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-25
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Database references