1FFR

CRYSTAL STRUCTURE OF CHITINASE A MUTANT Y390F COMPLEXED WITH HEXA-N-ACETYLCHITOHEXAOSE (NAG)6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

High resolution structural analyses of mutant chitinase A complexes with substrates provide new insight into the mechanism of catalysis.

Papanikolau, Y.Prag, G.Tavlas, G.Vorgias, C.E.Oppenheim, A.B.Petratos, K.

(2001) Biochemistry 40: 11338-11343

  • Primary Citation of Related Structures:  1EHN, 1EIB

  • PubMed Abstract: 
  • Chitinase A (ChiA) from the bacterium Serratia marcescens is a hydrolytic enzyme, which cleaves beta-1,4-glycosidic bonds of the natural biopolymer chitin to generate di-N-acetyl-chitobiose. The refined structure of ChiA at 1.55 A shows that residue ...

    Chitinase A (ChiA) from the bacterium Serratia marcescens is a hydrolytic enzyme, which cleaves beta-1,4-glycosidic bonds of the natural biopolymer chitin to generate di-N-acetyl-chitobiose. The refined structure of ChiA at 1.55 A shows that residue Asp313, which is located near the catalytic proton donor residue Glu315, is found in two alternative conformations of equal occupancy. In addition, the structures of the cocrystallized mutant proteins D313A, E315Q, Y390F, and D391A with octa- or hexa-N-acetyl-glucosamine have been refined at high resolution and the interactions with the substrate have been characterized. The obtained results clearly show that the active site is a semiclosed tunnel. Upon binding, the enzyme bends and rotates the substrate in the vicinity of the scissile bond. Furthermore, the enzyme imposes a critical "chair" to "boat" conformational change on the sugar residue bound to the -1 subsite. According to our results, we suggest that residues Asp313 and Tyr390 along with Glu315 play a central role in the catalysis. We propose that after the protonation of the substrate glycosidic bond, Asp313 that interacts with Asp311 flips to its alternative position where it interacts with Glu315 thus forcing the substrate acetamido group of -1 sugar to rotate around the C2-N2 bond. As a result of these structural changes, the water molecule that is hydrogen-bonded to Tyr390 and the NH of the acetamido group is displaced to a position that allows the completion of hydrolysis. The presented results suggest a mechanism for ChiA that modifies the earlier proposed "substrate assisted" catalysis.


    Related Citations: 
    • CDE NOVO PURIFICATION SCHEME AND CRYSTALLIZATION CONDITIONS YIELD HIGH-RESOLUTION STRUCTURES OF CHITINASE A AND ITS COMPLEX WITH THE INHIBITOR ALLOSAMIDIN
      Papanikolau, Y.,Tavlas, G.,Vorgias, C.E.,Petratos, K.
      (2003) Acta Crystallogr.,Sect.D 59: 400
    • Crystal Structure of a bacterial chitinase at 2.3 Angstrom resolution
      Perrakis, A.,Tews, I.,Dauter, Z.,Oppenheim, A.B.,Chet, I.,Wilson, K.S.,Vorgias, C.E.
      (1994) Structure 2: 1169


    Organizational Affiliation

    Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, P.O. Box 1527, 71110 Heraklion, Greece.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHITINASE A
A
540Serratia marcescensGene Names: chiA
EC: 3.2.1.14
Find proteins for P07254 (Serratia marcescens)
Go to UniProtKB:  P07254
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.183 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 200.172α = 90.00
b = 131.921β = 90.00
c = 59.268γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-09-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description