Crystal structure of human chitotriosidase-1 catalytic domain at 1.0 A resolution

Experimental Data Snapshot

  • Resolution: 1.00 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.136 

Starting Model: experimental
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New insights into the enzymatic mechanism of human chitotriosidase (CHIT1) catalytic domain by atomic resolution X-ray diffraction and hybrid QM/MM

Fadel, F.Zhao, Y.Cachau, R.Cousido-Siah, A.Ruiz, F.X.Harlos, K.Howard, E.Mitschler, A.Podjarny, A.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1455-1470

  • DOI: https://doi.org/10.1107/S139900471500783X
  • Primary Citation of Related Structures:  
    4WJX, 4WK9, 4WKA, 4WKF, 4WKH

  • PubMed Abstract: 

    Chitotriosidase (CHIT1) is a human chitinase belonging to the highly conserved glycosyl hydrolase family 18 (GH18). GH18 enzymes hydrolyze chitin, an N-acetylglucosamine polymer synthesized by lower organisms for structural purposes. Recently, CHIT1 has attracted attention owing to its upregulation in immune-system disorders and as a marker of Gaucher disease. The 39 kDa catalytic domain shows a conserved cluster of three acidic residues, Glu140, Asp138 and Asp136, involved in the hydrolysis reaction. Under an excess concentration of substrate, CHIT1 and other homologues perform an additional activity, transglycosylation. To understand the catalytic mechanism of GH18 chitinases and the dual enzymatic activity, the structure and mechanism of CHIT1 were analyzed in detail. The resolution of the crystals of the catalytic domain was improved from 1.65 Å (PDB entry 1waw) to 0.95-1.10 Å for the apo and pseudo-apo forms and the complex with chitobiose, allowing the determination of the protonation states within the active site. This information was extended by hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. The results suggest a new mechanism involving changes in the conformation and protonation state of the catalytic triad, as well as a new role for Tyr27, providing new insights into the hydrolysis and transglycosylation activities.

  • Organizational Affiliation

    Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chitotriosidase-1377Homo sapiensMutation(s): 0 
Gene Names: CHIT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13231 (Homo sapiens)
Explore Q13231 
Go to UniProtKB:  Q13231
GTEx:  ENSG00000133063 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13231
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.00 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.136 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.69α = 90
b = 105.749β = 90
c = 41.528γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Database references
  • Version 1.2: 2015-07-22
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description