1UR9

Interactions of a family 18 chitinase with the designed inhibitor HM508, and its degradation product, chitobiono-delta-lactone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Interactions of a Family 18 Chitinase with the Designed Inhibitor Hm508 and its Degradation Product, Chitobiono-Delta-Lactone.

Vaaje-Kolstad, G.Vasella, A.Peter, M.G.Netter, C.Houston, D.R.Westereng, B.Synstad, B.Eijsink, V.G.H.Van Aalten, D.M.F.

(2004) J.Biol.Chem. 279: 3612

  • DOI: 10.1074/jbc.M310057200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe enzymological and structural analyses of the interaction between the family 18 chitinase ChiB from Serratia marcescens and the designed inhibitor N,N'-diacetylchitobionoxime-N-phenylcarbamate (HM508). HM508 acts as a competitive inhibitor ...

    We describe enzymological and structural analyses of the interaction between the family 18 chitinase ChiB from Serratia marcescens and the designed inhibitor N,N'-diacetylchitobionoxime-N-phenylcarbamate (HM508). HM508 acts as a competitive inhibitor of this enzyme with a K(i) in the 50 microM range. Active site mutants of ChiB show K(i) values ranging from 1 to 200 microM, providing insight into some of the interactions that determine inhibitor affinity. Interestingly, the wild type enzyme slowly degrades HM508, but the inhibitor is essentially stable in the presence of the moderately active D142N mutant of ChiB. The crystal structure of the D142N-HM508 complex revealed that the two sugar moieties bind to the -2 and -1 subsites, whereas the phenyl group interacts with aromatic side chains that line the +1 and +2 subsites. Enzymatic degradation of HM508, as well as a Trp --> Ala mutation in the +2 subsite of ChiB, led to reduced affinity for the inhibitor, showing that interactions between the phenyl group and the enzyme contribute to binding. Interestingly, a complex of enzymatically degraded HM508 with the wild type enzyme showed a chitobiono-delta-lactone bound in the -2 and -1 subsites, despite the fact that the equilibrium between the lactone and the hydroxy acid forms in solution lies far toward the latter. This shows that the active site preferentially binds the (4)E conformation of the -1 sugar, which resembles the proposed transition state of the reaction.


    Related Citations: 
    • Structural Insights Into the Catalytic Mechansim of a 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.USA 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.,Eijsink, V.G.H.,Wierenga, R.K.
      (2000) Proc.Natl.Acad.Sci.USA 97: 5842


    Organizational Affiliation

    Department of Chemistry and Biotechnology, Agricultural University of Norway, N-1432 As, Norway.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHITINASE B
A, B
499Serratia marcescensMutation(s): 1 
Gene Names: chiB
Find proteins for Q54276 (Serratia marcescens)
Go to UniProtKB:  Q54276
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PHJ
Query on PHJ

Download SDF File 
Download CCD File 
A, B
N-[(AMINOOXY)CARBONYL]-N-PHENYLAMINE
N-[(AMINOOXY)CARBONYL]ANILINE
C7 H8 N2 O2
YQHOHPOCZUAUKP-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GDL
Query on GDL

Download SDF File 
Download CCD File 
A, B
2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-LACTONE
C8 H13 N O6
NELQYZRSPDCGRQ-DBRKOABJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.524α = 90.00
b = 104.177β = 90.00
c = 185.992γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-27
    Type: Initial release
  • Version 1.1: 2015-04-15
    Type: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance