1NKG

Rhamnogalacturonan lyase from Aspergillus aculeatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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. T ...

    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.,Sect.D 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rhamnogalacturonase B
A
508Aspergillus aculeatusGene Names: rglA (RGL4)
EC: 4.2.2.23
Find proteins for Q00019 (Aspergillus aculeatus)
Go to UniProtKB:  Q00019
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.164 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.009α = 90.00
b = 77.009β = 90.00
c = 170.787γ = 90.00
Software Package:
Software NamePurpose
RESOLVEphasing
SCALEPACKdata scaling
SOLVEphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-25
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance