5G56

THE TETRA-MODULAR CELLULOSOMAL ARABINOXYLANASE CtXyl5A STRUCTURE AS REVEALED BY X-RAY CRYSTALLOGRAPHY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Mechanism by which Arabinoxylanases Can Recognise Highly Decorated Xylans.

Labourel, A.Crouch, L.I.Bras, J.L.Jackson, A.Rogowski, A.Gray, J.Yadav, M.P.Henrissat, B.Fontes, C.M.Gilbert, H.J.Najmudin, S.Basle, A.Cuskin, F.

(2016) J.Biol.Chem. 291: 22149

  • DOI: 10.1074/jbc.M116.743948
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The enzymatic degradation of plant cell walls is an important biological process of increasing environmental and industrial significance. Xylan, a major component of the plant cell wall, consists of a backbone of β-1,4-xylose (Xylp) units that are of ...

    The enzymatic degradation of plant cell walls is an important biological process of increasing environmental and industrial significance. Xylan, a major component of the plant cell wall, consists of a backbone of β-1,4-xylose (Xylp) units that are often decorated with arabinofuranose (Araf) side chains. A large penta-modular enzyme, CtXyl5A, was shown previously to specifically target arabinoxylans. The mechanism of substrate recognition displayed by the enzyme, however, remains unclear. Here we report the crystal structure of the arabinoxylanase and the enzyme in complex with ligands. The data showed that four of the protein modules adopt a rigid structure, which stabilizes the catalytic domain. The C-terminal non-catalytic carbohydrate binding module could not be observed in the crystal structure, suggesting positional flexibility. The structure of the enzyme in complex with Xylp-β-1,4-Xylp-β-1,4-Xylp-[α-1,3-Araf]-β-1,4-Xylp showed that the Araf decoration linked O 3 to the xylose in the active site is located in the pocket (-2* subsite) that abuts onto the catalytic center. The -2* subsite can also bind to Xylp and Arap, explaining why the enzyme can utilize xylose and arabinose as specificity determinants. Alanine substitution of Glu 68 , Tyr 92 , or Asn 139 , which interact with arabinose and xylose side chains at the -2* subsite, abrogates catalytic activity. Distal to the active site, the xylan backbone makes limited apolar contacts with the enzyme, and the hydroxyls are solvent-exposed. This explains why CtXyl5A is capable of hydrolyzing xylans that are extensively decorated and that are recalcitrant to classic endo-xylanase attack.


    Related Citations: 
    • Purification, Crystallization and Preliminary X-Ray Characterization of the Pentamodular Arabinoxylanase Ctxyl5A from Clostridium Thermocellum.
      Bras, J.L.A.,Correia, M.A.S.,Romao, M.J.,Prates, J.A.M.,Fontes, C.M.G.A.,Najmudin, S.
      (2011) Acta Crystallogr.,Sect.F 67: 833


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, UMR7857 CNRS, Aix-Marseille University, F-13288 Marseille, France, USC1408 Architecture et Fonction des Macromolécules Biologiques, INRA, F-13288 Marseille, France, and the Department of Biological Sciences, King Abdulaziz University, Jedda 21589, Saudi Arabia.,CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal, NZYTech Genes & Enzymes, 1649-038 Lisboa, Portugal.,CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal, shabir@fmv.ulosboa.pt.,From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom, arnaud.basle@ncl.uk.,From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom.,the Eastern Regional Research Center, United States Department of Agriculture-Agricultural Research Service, Wyndmoor, Pennsylvania 19038.,From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom, Fiona.cuskin@newcastle.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBOHYDRATE BINDING FAMILY 6
A
862Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)Mutation(s): 0 
Find proteins for A3DHG6 (Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Go to UniProtKB:  A3DHG6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.237 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 147.410α = 90.00
b = 191.730β = 90.00
c = 50.700γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
SCALAdata scaling
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-07-06
    Type: Other
  • Version 1.2: 2016-08-31
    Type: Database references
  • Version 1.3: 2016-11-09
    Type: Database references