3G6M

crystal structure of a chitinase CrChi1 from the nematophagous fungus Clonostachys rosea in complex with a potent inhibitor caffeine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure and mutagenesis analysis of chitinase CrChi1 from the nematophagous fungus Clonostachys rosea in complex with the inhibitor caffeine

Yang, J.Gan, Z.Lou, Z.Tao, N.Mi, Q.Liang, L.Sun, Y.Guo, Y.Huang, X.Zou, C.Rao, Z.Meng, Z.Zhang, K.-Q.

(2010) Microbiology 156: 3566-3574

  • DOI: 10.1099/mic.0.043653-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chitinases are a group of enzymes capable of hydrolysing the β-(1,4)-glycosidic bonds of chitin, an essential component of the fungal cell wall, the shells of nematode eggs, and arthropod exoskeletons. Chitinases from pathogenic fungi have been shown ...

    Chitinases are a group of enzymes capable of hydrolysing the β-(1,4)-glycosidic bonds of chitin, an essential component of the fungal cell wall, the shells of nematode eggs, and arthropod exoskeletons. Chitinases from pathogenic fungi have been shown to be putative virulence factors, and can play important roles in infecting hosts. However, very limited information is available on the structure of chitinases from nematophagous fungi. Here, we present the 1.8 Å resolution of the first structure of a Family 18 chitinase from this group of fungi, that of Clonostachys rosea CrChi1, and the 1.6 Å resolution of CrChi1 in complex with a potent inhibitor, caffeine. Like other Family 18 chitinases, CrChi1 has the DXDXE motif at the end of strand β5, with Glu174 as the catalytic residue in the middle of the open end of the (β/α)(8) barrel. Two caffeine molecules were shown to bind to CrChi1 in subsites -1 to +1 in the substrate-binding domain. Moreover, site-directed mutagenesis of the amino acid residues forming hydrogen bonds with caffeine molecules suggests that these residues are important for substrate binding and the hydrolytic process. Our results provide a foundation for elucidating the catalytic mechanism of chitinases from nematophagous fungi and for improving the pathogenicity of nematophagous fungi against agricultural pest hosts.


    Organizational Affiliation

    Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chitinase
A
406Bionectria ochroleucaMutation(s): 0 
Gene Names: Crchi1
Find proteins for A9LI60 (Bionectria ochroleuca)
Go to UniProtKB:  A9LI60
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CFF
Query on CFF

Download SDF File 
Download CCD File 
A
CAFFEINE
3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE
C8 H10 N4 O2
RYYVLZVUVIJVGH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CFFKi: 19700000 nM BINDINGMOAD
CFFKi: 19700000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.161α = 90.00
b = 72.038β = 91.24
c = 59.298γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MAR345dtbdata collection
HKL-2000data scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance