3NJV

Rhamnogalacturonan lyase from Aspergillus aculeatus K150A substrate complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural and Biochemical Studies Elucidate the Mechanism of Rhamnogalacturonan Lyase from Aspergillus aculeatus.

Jensen, M.H.Otten, H.Christensen, U.Borchert, T.V.Christensen, L.L.Larsen, S.Leggio, L.L.

(2010) J Mol Biol 404: 100-111

  • DOI: 10.1016/j.jmb.2010.09.013
  • Primary Citation of Related Structures:  
    2XHN, 3NJV, 3NJX

  • PubMed Abstract: 
  • We present here the first experimental evidence for bound substrate in the active site of a rhamnogalacturonan lyase belonging to family 4 of polysaccharide lyases, Aspergillus aculeatus rhamnogalacturonan lyase (RGL4). RGL4 is involved in the degradation of rhamnogalacturonan-I, an important pectic plant cell wall polysaccharide ...

    We present here the first experimental evidence for bound substrate in the active site of a rhamnogalacturonan lyase belonging to family 4 of polysaccharide lyases, Aspergillus aculeatus rhamnogalacturonan lyase (RGL4). RGL4 is involved in the degradation of rhamnogalacturonan-I, an important pectic plant cell wall polysaccharide. Based on the previously determined wild-type structure, enzyme variants RGL4_H210A and RGL4_K150A have been produced and characterized both kinetically and structurally, showing that His210 and Lys150 are key active-site residues. Crystals of the RGL4_K150A variant soaked with a rhamnogalacturonan digest gave a clear picture of substrate bound in the -3/+3 subsites. The crystallographic and kinetic studies on RGL4, and structural and sequence comparison to other enzymes in the same and other PL families, enable us to propose a detailed reaction mechanism for the β-elimination on [-,2)-α-l-rhamno-(1,4)-α-d-galacturonic acid-(1,-]. The mechanism differs significantly from the one established for pectate lyases, in which most often calcium ions are engaged in catalysis.


    Organizational Affiliation

    Biophysical Chemistry Group, Department of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Rhamnogalacturonase BA508Aspergillus aculeatusMutation(s): 1 
Gene Names: rhgBrglARGL4
EC: 4.2.2.10 (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
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-rhamnopyranose-(1-4)-beta-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranose-(1-4)-beta-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranose-(1-4)-beta-D-galactopyranuronic acidB 6N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G54644MH
GlyCosmos:  G54644MH
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.974α = 90
b = 76.974β = 90
c = 170.649γ = 90
Software Package:
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Data collection, Refinement description
  • Version 1.3: 2020-04-15
    Changes: Data collection, Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary