1OGB

Chitinase b from Serratia marcescens mutant D142N


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the D142N Mutant of the Family 18 Chitinase Chib from Serratia Marcescens and its Complex with Allosamidin

Vaaje-Kolstad, G.Houston, D.R.Rao, F.V.Peter, M.G.Synstad, B.van Aalten, D.M.F.Eijsink, V.G.H.

(2004) Biochim Biophys Acta 1696: 103-111

  • DOI: 10.1016/j.bbapap.2003.09.014
  • Primary Citation of Related Structures:  
    1OGG, 1OGB

  • PubMed Abstract: 
  • Catalysis by ChiB, a family 18 chitinase from Serratia marcescens, involves a conformational change of Asp142 which is part of a characteristic D(140)XD(142)XE(144) sequence motif. In the free enzyme Asp142 points towards Asp140, whereas it rotates t ...

    Catalysis by ChiB, a family 18 chitinase from Serratia marcescens, involves a conformational change of Asp142 which is part of a characteristic D(140)XD(142)XE(144) sequence motif. In the free enzyme Asp142 points towards Asp140, whereas it rotates towards the catalytic acid, Glu144, upon ligand binding. Mutation of Asp142 to Asn reduced k(cat) and affinity for allosamidin, a competitive inhibitor. The X-ray structure of the D142N mutant showed that Asn142 points towards Glu144 in the absence of a ligand. The active site also showed other structural adjustments (Tyr10, Ser93) that had previously been observed in the wild-type enzyme upon substrate binding. The X-ray structure of a complex of D142N with allosamidin, a pseudotrisaccharide competitive inhibitor, was essentially identical to that of the wild-type enzyme in complex with the same compound. Thus, the reduced allosamidin affinity in the mutant is not caused by structural changes but solely by the loss of electrostatic interactions with Asp142. The importance of electrostatics was further confirmed by the pH dependence of catalysis and allosamidin inhibition. The pH-dependent apparent affinities for allosamidin were not correlated with k(cat), indicating that it is probably better to view the inhibitor as a mimic of the oxazolinium ion reaction intermediate than as a transition state analogue.


    Related Citations: 
    • Structural Insights Into the Catalytic Mechanism of Family 18 Exochitinase
      van Aalten, D.M.F., Komander, D., Synstad, B., Gaseidnes, S., Peter, M.G., Eijsink, V.G.H.
      (2001) Proc Natl Acad Sci U S A 98: 8979
    • Structure of a Two-Domain Chitotriosidase from Serratia Marcescens at 1.9 A Resolution
      van Aalten, D.M.F., Synstad, B., Brurberg, M.B., Hough, E., Riise, B.W., Eijsink, V.G.H., Wierenga, R.K.
      (2000) Proc Natl Acad Sci U S A 97: 5842

    Organizational Affiliation

    Department of Chemistry and Biotechnology, Agricultural University of Norway, PO Box 5040, N-1432 Aas, Norway.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CHITINASE BAB499Serratia marcescensMutation(s): 1 
Gene Names: chiB
EC: 3.2.1.14
Find proteins for P11797 (Serratia marcescens)
Explore P11797 
Go to UniProtKB:  P11797
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.948α = 90
b = 103.978β = 90
c = 186.458γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-28
    Changes: Advisory, Database references, Source and taxonomy, Structure summary