5AOS

Structure of a novel carbohydrate binding module from Ruminococcus flavefaciens FD-1 endoglucanase Cel5A solved at the As edge


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.126 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Complexity of the Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition.

Venditto, I.Luis, A.S.Rydahl, M.Schuckel, J.Fernandes, V.O.Vidal-Melgosa, S.Bule, P.Goyal, A.Pires, V.M.Dourado, C.G.Ferreira, L.M.Coutinho, P.M.Henrissat, B.Knox, J.P.Basle, A.Najmudin, S.Gilbert, H.J.Willats, W.G.Fontes, C.M.

(2016) Proc. Natl. Acad. Sci. U.S.A. 113: 7136-7141

  • DOI: 10.1073/pnas.1601558113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The breakdown of plant cell wall (PCW) glycans is an important biological and industrial process. Noncatalytic carbohydrate binding modules (CBMs) fulfill a critical targeting function in PCW depolymerization. Defining the portfolio of CBMs, the CBMo ...

    The breakdown of plant cell wall (PCW) glycans is an important biological and industrial process. Noncatalytic carbohydrate binding modules (CBMs) fulfill a critical targeting function in PCW depolymerization. Defining the portfolio of CBMs, the CBMome, of a PCW degrading system is central to understanding the mechanisms by which microbes depolymerize their target substrates. Ruminococcus flavefaciens, a major PCW degrading bacterium, assembles its catalytic apparatus into a large multienzyme complex, the cellulosome. Significantly, bioinformatic analyses of the R. flavefaciens cellulosome failed to identify a CBM predicted to bind to crystalline cellulose, a key feature of the CBMome of other PCW degrading systems. Here, high throughput screening of 177 protein modules of unknown function was used to determine the complete CBMome of R. flavefaciens The data identified six previously unidentified CBM families that targeted β-glucans, β-mannans, and the pectic polysaccharide homogalacturonan. The crystal structures of four CBMs, in conjunction with site-directed mutagenesis, provide insight into the mechanism of ligand recognition. In the CBMs that recognize β-glucans and β-mannans, differences in the conformation of conserved aromatic residues had a significant impact on the topology of the ligand binding cleft and thus ligand specificity. A cluster of basic residues in CBM77 confers calcium-independent recognition of homogalacturonan, indicating that the carboxylates of galacturonic acid are key specificity determinants. This report shows that the extended repertoire of proteins in the cellulosome of R. flavefaciens contributes to an extended CBMome that supports efficient PCW degradation in the absence of CBMs that specifically target crystalline cellulose.


    Related Citations: 
    • Purification and Crystallographic Studies of a Putative Carbohydrate-Binding Module from the Ruminococcus Flavefaciens Fd-1 Endoglucanase Cel5A.
      Pires, A.J.,Ribeiro, T.,Thompson, A.,Venditto, I.,Fernandes, V.O.,Bule, P.,Santos, H.,Alves, V.D.,Pires, V.,Ferreira, L.M.A.,Fontes, C.M.G.A.,Najmudin, S.
      (2015) Acta Crystallogr.,Sect.F 71: 958


    Organizational Affiliation

    Interdisciplinary Centre of Research in Animal Health, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário do Alto da Ajuda, 1300-477 Lisbon, Portugal; Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbohydrate binding module
A
106Ruminococcus flavefaciensMutation(s): 0 
Find proteins for A0A1A9TAF3 (Ruminococcus flavefaciens)
Go to UniProtKB:  A0A1A9TAF3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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

Download SDF File 
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: 1.29 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.126 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.393α = 90.00
b = 45.214β = 90.00
c = 49.563γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SHELXphasing
PHASERphasing
XDSdata reduction
Aimlessdata scaling

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: 2016-07-13
    Type: Database references
  • Version 1.2: 2018-12-05
    Type: Data collection, Database references, Source and taxonomy, Structure summary