Structure of the Thermotoga maritima Family 5 endo-glucanase in complex with 1-deoxynojiromycin

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 

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Structure of an iminosugar complex of a glycoside hydrolase family 5 lichenase provides insights into the active site.

Garg, P.Manoj, N.

(2023) Biochimie 204: 69-77

  • DOI: https://doi.org/10.1016/j.biochi.2022.09.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    TmCel5B is a lichenase belonging to glycoside hydrolase family 5 subfamily 36 (GH5_36). To gain insights into the active site of this subfamily which contains multifunctional endoglycanases, we determined the crystal structure of TmCel5B in complex with an iminosugar, 1-deoxynojiromycin (DNJ). DNJ is bound to the -1 subsite, making a network of non-covalent interactions with the acid/base residue Glu139, the nucleophile Glu259, and with other residues that are conserved across the GH5 family. The catalytic site displayed a Glu-Arg-Glu triad of the catalytic glutamates that is unique to the GH5_36 subfamily. Structural comparison of active sites of GH5_36 homologs revealed divergent residues and loop regions that are likely molecular determinants of homolog-specific properties. Furthermore, a comparative analysis of the binding modes of iminocyclitol complexes of GH5 homologs revealed the structural basis of their binding to GH5 glycosidases, in which the subsite binding location, the interactions of the ligand with specific conserved residues, and the electrostatic interactions of the catalytic glutamates with the ring nitrogen, are crucial.

  • Organizational Affiliation

    Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
341Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: TM_1752
Find proteins for Q9X274 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X274 
Go to UniProtKB:  Q9X274
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X274
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.33α = 90
b = 62.28β = 90
c = 202.69γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaBT/PR-13040/FNS/20/416/2009

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references
  • Version 1.2: 2023-01-25
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description