4UZ8

The SeMet structure of the family 46 carbohydrate-binding module (CBM46) of endo-beta-1,4-glucanase B (Cel5B) from Bacillus halodurans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.204 

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

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDO-BETA-1,4-GLUCANASE (CELULASE B)
A, B
130Bacillus 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.204 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 120.850α = 90.00
b = 120.850β = 90.00
c = 76.380γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXphasing
FAST_DPdata 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