4V2X

High resolution structure of the full length tri-modular endo-beta-1, 4-glucanase B (Cel5B) from Bacillus halodurans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Family 46 Carbohydrate-Binding Modules Contribute to the Enzymatic Hydrolysis of Xyloglucan and Beta-1,3-1,4-Glucans Through Distinct Mechanisms.

Venditto, I.Najmudin, S.Luis, A.S.Ferreira, L.M.Sakka, K.Knox, J.P.Gilbert, H.J.Fontes, C.M.

(2015) J.Biol.Chem. 290: 10572

  • DOI: 10.1074/jbc.M115.637827
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Structural carbohydrates comprise an extraordinary source of energy that remains poorly utilized by the biofuel sector as enzymes have restricted access to their substrates within the intricacy of plant cell walls. Carbohydrate active enzymes (CAZYme ...

    Structural carbohydrates comprise an extraordinary source of energy that remains poorly utilized by the biofuel sector as enzymes have restricted access to their substrates within the intricacy of plant cell walls. Carbohydrate active enzymes (CAZYmes) that target recalcitrant polysaccharides are modular enzymes containing noncatalytic carbohydrate-binding modules (CBMs) that direct enzymes to their cognate substrate, thus potentiating catalysis. In general, CBMs are functionally and structurally autonomous from their associated catalytic domains from which they are separated through flexible linker sequences. Here, we show that a C-terminal CBM46 derived from BhCel5B, a Bacillus halodurans endoglucanase, does not interact with β-glucans independently but, uniquely, acts cooperatively with the catalytic domain of the enzyme in substrate recognition. The structure of BhCBM46 revealed a β-sandwich fold that abuts onto the region of the substrate binding cleft upstream of the active site. BhCBM46 as a discrete entity is unable to bind to β-glucans. Removal of BhCBM46 from BhCel5B, however, abrogates binding to β-1,3-1,4-glucans while substantially decreasing the affinity for decorated β-1,4-glucan homopolymers such as xyloglucan. The CBM46 was shown to contribute to xyloglucan hydrolysis only in the context of intact plant cell walls, but it potentiates enzymatic activity against purified β-1,3-1,4-glucans in solution or within the cell wall. This report reveals the mechanism by which a CBM can promote enzyme activity through direct interaction with the substrate or by targeting regions of the plant cell wall where the target glucan is abundant.


    Related Citations: 
    • Overproduction, Purification, Crystallization and Preliminary X-Ray Characterization of the Family 46 Carbohydrate-Binding Module (Cbm46) of Endo-Beta-1,4-Glucanase B (Celb) from Bacillus Halodurans.
      Venditto, I.,Santos, H.,Ferreira, L.M.A.,Sakka, K.,Fontes, C.M.G.A.,Najmudin, S.
      (2014) Acta Crystallogr.,Sect.F 70: 754


    Organizational Affiliation

    the Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom.,From the Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal, cafontes@fmv.ulisboa.pt.,the Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom, harry.gilbert@newcastle.ac.uk.,From the Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal.,the Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.,the Graduate School of Bioresources, Mie University, Tsu 514-8507, Japan, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDO-BETA-1,4-GLUCANASE (CELLULASE B)
A
597Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)Mutation(s): 0 
Find proteins for Q9KF82 (Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Go to UniProtKB:  Q9KF82
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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

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Download CCD File 
A
CACODYLATE ION
dimethylarsinate
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.154 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 74.220α = 90.00
b = 141.840β = 90.00
c = 50.820γ = 90.00
Software Package:
Software NamePurpose
BALBESphasing
XDSdata reduction
xia2data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2015-03-11
    Type: Database references
  • Version 1.2: 2015-05-13
    Type: Database references