1KR0

Hevamine Mutant D125A/Y183F in Complex with Tetra-NAG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.175 

wwPDB Validation 3D Report Full Report



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

  • DOI: 10.1046/j.0014-2956.2001.02721.x
  • Primary Citation of Related Structures:  
    1KR1, 1KR0, 1KQZ, 1KQY

  • 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 wild-type enzyme and mutants of these residues as inclusion bodies in Escherichia coli ...

    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: 
    • 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
    • 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
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hevamine AA273Hevea brasiliensisMutation(s): 2 
EC: 3.2.1.14 (PDB Primary Data), 3.2.1.17 (PDB Primary Data)
Find proteins for P23472 (Hevea brasiliensis)
Explore P23472 
Go to UniProtKB:  P23472
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
4 N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.945α = 90
b = 57.57β = 90
c = 82.415γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary