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Crystal Structure Analysis of the 6-Oxo Camphor Hydrolase His122Ala Mutant Bound to Its Natural Product (2S,4S)-alpha-Campholinic Acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of 6-oxo camphor hydrolase H122A mutant bound to its natural product, (2S,4S)-alpha-campholinic acid: mutant structure suggests an atypical mode of transition state binding for a crotonase homolog.

Leonard, P.M.Grogan, G.

(2004) J.Biol.Chem. 279: 31312-31317

  • DOI: 10.1074/jbc.M403514200

  • PubMed Abstract: 
  • The crotonase homolog, 6-oxo camphor hydrolase (OCH), catalyzes the desymmetrization of bicyclic beta-diketones to optically active keto acids via an enzymatic retro-Claisen reaction, resulting in the cleavage of a carbon-carbon bond. We have previou ...

    The crotonase homolog, 6-oxo camphor hydrolase (OCH), catalyzes the desymmetrization of bicyclic beta-diketones to optically active keto acids via an enzymatic retro-Claisen reaction, resulting in the cleavage of a carbon-carbon bond. We have previously reported the structure of OCH (Whittingham, J. L., Turkenburg, J. P., Verma, C. S., Walsh, M. A., and Grogan, G. (2003) J. Biol. Chem. 278, 1744-1750), which suggested the involvement of five residues, His-45, His-122, His-145, Asp-154, and Glu-244, in catalysis. Here we report mutation studies on OCH that reveal that H145A and D154N mutants of OCH have greatly reduced values of k(cat)/K(m) derived from a very large increase in K(m) for the native substrate, 6-oxo camphor. In addition, H122A has a greatly reduced value of k(cat), and its K(m) is five times that of the wild-type. The location of the active site is confirmed by the 1.9-A structure of the H122A mutant of OCH complexed with the minor diastereoisomer of (2S,4S)-alpha-campholinic acid, the natural product of the enzyme. This shows the pendant acetate of the product hydrogen bonded to a His-145/Asp-154 dyad and the endocyclic carbonyl of the cyclopentane ring hydrogen bonded to Trp-40. The results are suggestive of a base-catalyzed mechanism of C-C bond cleavage and provide clues to the origin of prochiral selectivity by the enzyme and to the recruitment of the crotonase fold for alternate modes of transition state stabilization to those described for other crotonase superfamily members.


    Related Citations: 
    • The 2- Crystal Structure of 6-Oxo Camphor Hydrolase. NEW STRUCTURAL DIVERSITY IN THE CROTONASE SUPERFAMILY.
      Whittingham, J.L.,Turkenburg, J.P.,Verma, C.S.,Walsh, M.A.,Grogan, G.
      (2003) J.Biol.Chem. 278: 1744
    • An Asymmetric Enzyme-Catalysed Retro-Claisen Reaction for the Desymmetrisation of Cyclic beta-Diketones.
      Grogan, G.,Graf, J.,Jones, A.,Parsons, S.,Turner, N.J.,Flitsch, S.L.
      (2001) Angew.Chem.Int.Ed.Engl. 40: 1111
    • The Desymmetrization of Bicyclic beta-Diketones by an Enzymatic Retro-Claisen Reaction. A NEW REACTION OF THE CROTONASE SUPERFAMILY.
      Grogan, G.,Roberts, G.A.,Bougioukou, D.,Turner, N.J.,Flitsch, S.L.
      (2001) J.Biol.Chem. 276: 12565


    Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-oxocamphor hydrolase
A, B, C, D, E, F, G, H, I, J, K, L
257Rhodococcus spMutation(s): 1 
Gene Names: camK
EC: 3.7.1.18
Find proteins for Q93TU6 (Rhodococcus sp)
Go to UniProtKB:  Q93TU6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B, F, I, K
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CAX
Query on CAX

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
(2S,4S)-4-(2,2-DIHYDROXYETHYL)-2,3,3-TRIMETHYLCYCLOPENTANONE
(2S,4S)-ALPHA-CAMPHOLINIC ACID
C10 H18 O3
KAXFPJKKGITBPU-RQJHMYQMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 83.280α = 90.00
b = 132.008β = 94.11
c = 135.424γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-29
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance