Crystal structure of the sixth cohesin from Acetivibrio cellulolyticus' scaffoldin B in complex with Cel5 dockerin S15I, I16N mutant

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structure-function analyses generate novel specificities to assemble the components of multienzyme bacterial cellulosome complexes.

Bule, P.Cameron, K.Prates, J.A.M.Ferreira, L.M.A.Smith, S.P.Gilbert, H.J.Bayer, E.A.Najmudin, S.Fontes, C.M.G.A.Alves, V.D.

(2018) J Biol Chem 293: 4201-4212

  • DOI: https://doi.org/10.1074/jbc.RA117.001241
  • Primary Citation of Related Structures:  
    5NRK, 5NRM

  • PubMed Abstract: 

    The cellulosome is a remarkably intricate multienzyme nanomachine produced by anaerobic bacteria to degrade plant cell wall polysaccharides. Cellulosome assembly is mediated through binding of enzyme-borne dockerin modules to cohesin modules of the primary scaffoldin subunit. The anaerobic bacterium Acetivibrio cellulolyticus produces a highly intricate cellulosome comprising an adaptor scaffoldin, ScaB, whose cohesins interact with the dockerin of the primary scaffoldin (ScaA) that integrates the cellulosomal enzymes. The ScaB dockerin selectively binds to cohesin modules in ScaC that anchors the cellulosome onto the cell surface. Correct cellulosome assembly requires distinct specificities displayed by structurally related type-I cohesin-dockerin pairs that mediate ScaC-ScaB and ScaA-enzyme assemblies. To explore the mechanism by which these two critical protein interactions display their required specificities, we determined the crystal structure of the dockerin of a cellulosomal enzyme in complex with a ScaA cohesin. The data revealed that the enzyme-borne dockerin binds to the ScaA cohesin in two orientations, indicating two identical cohesin-binding sites. Combined mutagenesis experiments served to identify amino acid residues that modulate type-I cohesin-dockerin specificity in A. cellulolyticus Rational design was used to test the hypothesis that the ligand-binding surfaces of ScaA- and ScaB-associated dockerins mediate cohesin recognition, independent of the structural scaffold. Novel specificities could thus be engineered into one, but not both, of the ligand-binding sites of ScaB, whereas attempts at manipulating the specificity of the enzyme-associated dockerin were unsuccessful. These data indicate that dockerin specificity requires critical interplay between the ligand-binding surface and the structural scaffold of these modules.

  • Organizational Affiliation

    From the CIISA-Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, C
143Acetivibrio cellulolyticusMutation(s): 0 
Gene Names: cipV
Find proteins for Q9RPL0 (Acetivibrio cellulolyticus)
Explore Q9RPL0 
Go to UniProtKB:  Q9RPL0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RPL0
Sequence Annotations
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DocCel5: Type I dockerin repeat domain from A. cellulolyticus family 5 endoglucanase WP_010249057 S15I, I16N mutant
B, D
68Acetivibrio cellulolyticusMutation(s): 0 
Gene Names: BglC
Find proteins for A0A2R2JFJ6 (Acetivibrio cellulolyticus)
Explore A0A2R2JFJ6 
Go to UniProtKB:  A0A2R2JFJ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2R2JFJ6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
J [auth B],
O [auth D]
C3 H8 O3
Query on SCN

Download Ideal Coordinates CCD File 
H [auth B],
I [auth B],
K [auth C]
Query on CA

Download Ideal Coordinates CCD File 
E [auth B]
F [auth B]
G [auth B]
L [auth D]
M [auth D]
E [auth B],
F [auth B],
G [auth B],
L [auth D],
M [auth D],
N [auth D]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.539α = 90
b = 79.809β = 90
c = 112.159γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e TecnologiaPortugalEXPL/BIA-MIC/1176/2012
Fundacao para a Ciencia e TecnologiaPortugalPTDC/BIA-PRO/103980/2008
Fundacao para a Ciencia e TecnologiaPortugalPTDC/BIA-MIC/5947/2014

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-02-07
    Changes: Database references
  • Version 1.2: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description