3BH3

Crystal structure of acetoacetate decarboxylase from Chromobacterium violaceum in complex with acetyl acetone Schiff base intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The origin of the electrostatic perturbation in acetoacetate decarboxylase.

Ho, M.C.Menetret, J.F.Tsuruta, H.Allen, K.N.

(2009) Nature 459: 393-397

  • DOI: 10.1038/nature07938
  • Primary Citation of Related Structures:  
    3BGT, 3BH2, 3BH3

  • PubMed Abstract: 
  • Acetoacetate decarboxylase (AADase) has long been cited as the prototypical example of the marked shifts in the pK(a) values of ionizable groups that can occur in an enzyme active site. In 1966, it was hypothesized that in AADase the origin of the large pK(a) perturbation (-4 ...

    Acetoacetate decarboxylase (AADase) has long been cited as the prototypical example of the marked shifts in the pK(a) values of ionizable groups that can occur in an enzyme active site. In 1966, it was hypothesized that in AADase the origin of the large pK(a) perturbation (-4.5 log units) observed in the nucleophilic Lys 115 results from the proximity of Lys 116, marking the first proposal of microenvironment effects in enzymology. The electrostatic perturbation hypothesis has been demonstrated in a number of enzymes, but never for the enzyme that inspired its conception, owing to the lack of a three-dimensional structure. Here we present the X-ray crystal structures of AADase and of the enamine adduct with the substrate analogue 2,4-pentanedione. Surprisingly, the shift of the pK(a) of Lys 115 is not due to the proximity of Lys 116, the side chain of which is oriented away from the active site. Instead, Lys 116 participates in the structural anchoring of Lys 115 in a long, hydrophobic funnel provided by the novel fold of the enzyme. Thus, AADase perturbs the pK(a) of the nucleophile by means of a desolvation effect by placement of the side chain into the protein core while enforcing the proximity of polar residues, which facilitate decarboxylation through electrostatic and steric effects.


    Organizational Affiliation

    Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118-2394, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acetoacetate decarboxylaseA, B, C, D246Chromobacterium violaceum ATCC 12472Mutation(s): 0 
Gene Names: adcCV_3520
EC: 4.1.1.4
UniProt
Find proteins for Q7NSA6 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757))
Explore Q7NSA6 
Go to UniProtKB:  Q7NSA6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7NSA6
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
PNH PDBBind:  3BH3 Ki: 700 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.661α = 90
b = 105.661β = 90
c = 252.854γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2007-11-27 
  • Released Date: 2008-12-23 
  • Deposition Author(s): Ho, M., Allen, K.N.

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance