9HJ7 | pdb_00009hj7

Structure of Chitinase 35 from Metschnikowia pulcherrima (MpChit35)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.238 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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Literature

Structural-mechanistic insights and performance engineering of chitinase MpChit35 for tailored chito-oligosaccharide production.

Minguet-Lobato, M.Fernandez-Garcia, A.Jimenez-Ortega, E.Cervantes, F.V.Sanchez-Pozo, P.Plou, F.J.Sanz-Aparicio, J.Fernandez-Lobato, M.

(2025) Int J Biol Macromol 322: 146538-146538

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.146538
  • Primary Citation of Related Structures:  
    9HJ7

  • PubMed Abstract: 

    Chitinase-catalysed synthesis offers a promising biotechnological route for converting chitin-rich waste into value-added chito-oligosaccharides, whose biological activity depends on their degree of polymerization and acetylation, highlighting the need for precise enzymatic tools to tailor their structures. This study investigates the structural-functional determinants of the chitinase MpChit35 from Metschnikowia pulcherrima, which mainly produces di-acetyl-chitobiose ((GlcNAc) 2 ) and to a lesser extent tri-acetyl-chitotriose ((GlcNAc) 3 ) from chitin. Here the MpChit35 structure was solved at 2.55 Å and structural analysis combined with site-directed mutagenesis enabled the identification of key residues involved in substrate binding and catalysis. Thus, the L253R mutation significantly increased the protein catalytic efficiency and promoted near-exclusive production of (GlcNAc) 2 from chitin and oligomeric substrates, underscoring the role of polar interactions in defining the enzyme specificity and processivity. In contrast, the multiple-mutation A107D/D151N/A181S/M279A favoured the release of (GlcNAc) 3 and tetra-acetyl-chitotetraose. Furthermore, residue Trp73 contributed to an unusual distal substrate-binding platform and Ala107 resulted a key determinant for the product specificity. These findings provide mechanistic insights into chitinase function and support the rational design of enzymes with tailored cleavage patterns. This work contributes to the development of efficient biocatalysts for sustainable chitin valorisation and the industrial production of custom chito-oligosaccharides.


  • Organizational Affiliation
    • Department of Molecular Biology, Centre for Molecular Biology Severo Ochoa (CBM-CSIC-UAM), University Autonomous from Madrid. C/ Nicolás Cabrera, 1. Cantoblanco. 28049 Madrid, Spain; Institute of Catalysis (ICP-CSIC), C/ Marie Curie, 2. Cantoblanco. 28049 Madrid, Spain.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chitinase
A, B
291Metschnikowia pulcherrimaMutation(s): 0 
Gene Names: MPUL0D06620METSCH_D06620
UniProt
Find proteins for A0A8H7LG93 (Metschnikowia pulcherrima)
Explore A0A8H7LG93 
Go to UniProtKB:  A0A8H7LG93
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8H7LG93
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
H [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B],
L [auth B],
M [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.238 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.582α = 90
b = 54.85β = 107.72
c = 97.776γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2019-105838RB-C33
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2022-136367OB-C33

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release