Crystal structure of Caldicellulosiruptor saccharolyticus CBM27-1 in complex with mannohexaose

Experimental Data Snapshot

  • Resolution: 1.06 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 

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High-resolution crystal structures of Caldicellulosiruptor strain Rt8B.4 carbohydrate-binding module CBM27-1 and its complex with mannohexaose.

Roske, Y.Sunna, A.Pfeil, W.Heinemann, U.

(2004) J Mol Biol 340: 543-554

  • DOI: https://doi.org/10.1016/j.jmb.2004.04.072
  • Primary Citation of Related Structures:  
    1PMH, 1PMJ

  • PubMed Abstract: 

    Carbohydrate-binding modules (CBMs) are the most common non-catalytic modules associated with enzymes active in plant cell-wall hydrolysis. Despite the large number of putative CBMs being identified by amino acid sequence alignments, only few representatives have been experimentally shown to have a carbohydrate-binding function. Caldicellulosiruptor strain Rt8B.4 Man26 is a thermostable modular glycoside hydrolase beta-mannanase which contains two non-catalytic modules in tandem at its N terminus. These modules were recently shown to function primarily as beta-mannan-binding modules and have accordingly been classified as members of a novel family of CBMs, family 27. The N-terminal CBM27 (CsCBM27-1) of Man26 from Caldicellulosiruptor Rt8B.4 displays high-binding affinity towards mannohexaose with a Ka of 1 x 10(7) M(-1). Accordingly, the high-resolution crystal structures of CsCBM27-1 native and its mannohexaose complex were solved at 1.55 angstroms and 1.06 angstoms resolution, respectively. In the crystal, CsCBM27-1 shows the typical beta-sandwich jellyroll fold observed in other CBMs with a single metal ion bound, which was identified as calcium. The crystal structures reveal that the overall fold of CsCBM27-1 remains virtually unchanged upon sugar binding and that binding is mediated by three solvent-exposed tryptophan residues and few direct hydrogen bonds. Based on binding affinity and thermal unfolding experiments this structural calcium is shown to play a role in the thermal stability of CsCBM27-1 at high temperatures. The higher binding affinity of CsCBM27-1 to mannooligosaccharides when compared to other members of CBM family 27 might be explained by the different orientation of the residues forming the "aromatic platform" and by differences in the length of loops. Finally, evidence is presented, on the basis of fold similarities and the retention of the position of conserved motifs and a calcium ion, for the consolidation of related CBM families into a superfamily of CBMs.

  • Organizational Affiliation

    Crystallography Group, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, D-13125 Berlin, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
beta-1,4-mannanaseA [auth X]185Caldicellulosiruptor saccharolyticusMutation(s): 2 
Gene Names: manA
Find proteins for P77847 (Caldicellulosiruptor saccharolyticus)
Explore P77847 
Go to UniProtKB:  P77847
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP77847
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranoseB [auth A]6N/A
Glycosylation Resources
GlyTouCan:  G39448BE
GlyCosmos:  G39448BE
GlyGen:  G39448BE
Experimental Data & Validation

Experimental Data

  • Resolution: 1.06 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.281α = 90
b = 45.7β = 90
c = 110.113γ = 90
Software Package:
Software NamePurpose
MAR345data collection
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-22
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary