3HBE

Class IV chitinase structure from Picea abies at 1.55A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The first crystal structures of a family 19 class IV chitinase: the enzyme from Norway spruce.

Ubhayasekera, W.Rawat, R.Ho, S.W.Wiweger, M.Von Arnold, S.Chye, M.L.Mowbray, S.L.

(2009) Plant Mol.Biol. 71: 277-289

  • DOI: 10.1007/s11103-009-9523-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chitinases help plants defend themselves against fungal attack, and play roles in other processes, including development. The catalytic modules of most plant chitinases belong to glycoside hydrolase family 19. We report here x-ray structures of such ...

    Chitinases help plants defend themselves against fungal attack, and play roles in other processes, including development. The catalytic modules of most plant chitinases belong to glycoside hydrolase family 19. We report here x-ray structures of such a module from a Norway spruce enzyme, the first for any family 19 class IV chitinase. The bi-lobed structure has a wide cleft lined by conserved residues; the most interesting for catalysis are Glu113, the proton donor, and Glu122, believed to be a general base that activate a catalytic water molecule. Comparisons to class I and II enzymes show that loop deletions in the class IV proteins make the catalytic cleft shorter and wider; from modeling studies, it is predicted that only three N-acetylglucosamine-binding subsites exist in class IV. Further, the structural comparisons suggest that the family 19 enzymes become more closed on substrate binding. Attempts to solve the structure of the complete protein including the associated chitin-binding module failed, however, modeling studies based on close relatives indicate that the binding module recognizes at most three N-acetylglucosamine units. The combined results suggest that the class IV enzymes are optimized for shorter substrates than the class I and II enzymes, or alternatively, that they are better suited for action on substrates where only small regions of chitin chain are accessible. Intact spruce chitinase is shown to possess antifungal activity, which requires the binding module; removing this module had no effect on measured chitinase activity.


    Organizational Affiliation

    Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, 751 24 Uppsala, Sweden. wimal@xray.bmc.uu.se




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Class IV chitinase Chia4-Pa2
X
204Picea abiesMutation(s): 0 
EC: 3.2.1.14
Find proteins for Q6WSR8 (Picea abies)
Go to UniProtKB:  Q6WSR8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
X
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MXE
Query on MXE

Download SDF File 
Download CCD File 
X
2-METHOXYETHANOL
C3 H8 O2
XNWFRZJHXBZDAG-UHFFFAOYSA-N
 Ligand Interaction
FOR
Query on FOR

Download SDF File 
Download CCD File 
X
FORMYL GROUP
C H2 O
WSFSSNUMVMOOMR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 67.194α = 90.00
b = 65.792β = 90.00
c = 36.496γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
ADSCdata collection
REFMACphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance