1KR1

Hevamine Mutant D125A/E127A in Complex with Tetra-NAG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Expression and Characterization of Active Site Mutants of Hevamine, a Chitinase from the Rubber Tree Hevea brasiliensis.

Bokma, E.Rozeboom, H.J.Sibbald, M.Dijkstra, B.W.Beintema, J.J.

(2002) Eur.J.Biochem. 269: 893-901

  • Primary Citation of Related Structures:  1KQY, 1KQZ, 1KR0

  • PubMed Abstract: 
  • Hevamine is a chitinase from the rubber tree Hevea brasiliensis. Its active site contains Asp125, Glu127, and Tyr183, which interact with the -1 sugar residue of the substrate. To investigate their role in catalysis, we have successfully expressed wi ...

    Hevamine is a chitinase from the rubber tree Hevea brasiliensis. Its active site contains Asp125, Glu127, and Tyr183, which interact with the -1 sugar residue of the substrate. To investigate their role in catalysis, we have successfully expressed wild-type enzyme and mutants of these residues as inclusion bodies in Escherichia coli. After refolding and purification they were characterized by both structural and enzyme kinetic studies. Mutation of Tyr183 to phenylalanine produced an enzyme with a lower k(cat) and a slightly higher K(m) than the wild-type enzyme. Mutating Asp125 and Glu127 to alanine gave mutants with approximately 2% residual activity. In contrast, the Asp125Asn mutant retained substantial activity, with an approximately twofold lower k(cat) and an approximately twofold higher K(m) than the wild-type enzyme. More interestingly, it showed activity to higher pH values than the other variants. The X-ray structure of the Asp125Ala/Glu127Ala double mutant soaked with chitotetraose shows that, compared with wild-type hevamine, the carbonyl oxygen atom of the N-acetyl group of the -1 sugar residue has rotated away from the C1 atom of that residue. The combined structural and kinetic data show that Asp125 and Tyr183 contribute to catalysis by positioning the carbonyl oxygen of the N-acetyl group near to the C1 atom. This allows the stabilization of a positively charged transient intermediate, in agreement with a previous proposal that the enzyme makes use of substrate-assisted catalysis.


    Related Citations: 
    • Crystallization of Hevamine, an Enzyme with Lysozyme/Chitinase Activity from Hevea brasiliensis Latex.
      Rozeboom, H.J.,Budiani, A.,Beintema, J.J.,Dijkstra, B.W.
      (1990) J.Mol.Biol. 212: 441
    • Crystal Structures of Hevamine, a Plant Defence Protein with Chitinase and Lysozyme Activity, and its Complex with an Inhibitor.
      Terwisscha van Scheltinga, A.C.,Kalk, K.H.,Beintema, J.J.,Dijkstra, B.W.
      (1994) Structure 2: 1181
    • Stereochemistry of Chitin Hydrolysis by a Plant Chitinase/Lysozyme and X-ray Structure of a Complex with Allosamidin: Evidence for Substrate Assisted Catalysis.
      Terwisscha van Scheltinga, A.C.,Armand, S.,Kalk, K.H.,Isogai, A.,Henrissat, B.,Dijkstra, B.W.
      (1995) Biochemistry 34: 15619
    • The 1.8 A Resolution Structure of Hevamine, a Plant Chitinase/Lysozyme, and Analysis of the Conserved Sequence and Structure Motifs of Glycosyl Hydrolase Family 18.
      Terwisscha van Scheltinga, A.C.,Hennig, M.,Dijkstra, B.W.
      (1996) J.Mol.Biol. 262: 243


    Organizational Affiliation

    Department of Biochemistry, Rijksuniversiteit Groningen, The Netherlands. eb272@mole.bio.cam.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hevamine A
A
273Hevea brasiliensisEC: 3.2.1.17, 3.2.1.14
Find proteins for P23472 (Hevea brasiliensis)
Go to UniProtKB:  P23472
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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: 2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.795α = 90.00
b = 57.054β = 90.00
c = 81.671γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-23
    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