2PUH | pdb_00002puh

Crystal Structure of the S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with its substrate HOPDA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 
    0.203 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history

Literature

The Tautomeric Half-reaction of BphD, a C-C Bond Hydrolase: KINETIC AND STRUCTURAL EVIDENCE SUPPORTING A KEY ROLE FOR HISTIDINE 265 OF THE CATALYTIC TRIAD.

Horsman, G.P.Bhowmik, S.Seah, S.Y.Kumar, P.Bolin, J.T.Eltis, L.D.

(2007) J Biological Chem 282: 19894-19904

  • DOI: https://doi.org/10.1074/jbc.M702237200
  • Primary Citation Related Structures: 
    2PU5, 2PU7, 2PUH, 2PUJ, 2RI6

  • PubMed Abstract: 

    BphD of Burkholderia xenovorans LB400 catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to afford benzoic acid and 2-hydroxy-2,4-pentadienoic acid (HPD). An enol-keto tautomerization has been proposed to precede hydrolysis via a gem-diol intermediate. The role of the canonical catalytic triad (Ser-112, His-265, Asp-237) in mediating these two half-reactions remains unclear. We previously reported that the BphD-catalyzed hydrolysis of HOPDA (lambda(max) is 434 nm for the free enolate) proceeds via an unidentified intermediate with a red-shifted absorption spectrum (lambda(max) is 492 nm) (Horsman, G. P., Ke, J., Dai, S., Seah, S. Y. K., Bolin, J. T., and Eltis, L. D. (2006) Biochemistry 45, 11071-11086). Here we demonstrate that the S112A variant generates and traps a similar intermediate (lambda(max) is 506 nm) with a similar rate, 1/tau approximately 500 s(-1). The crystal structure of the S112A:HOPDA complex at 1.8-A resolution identified this intermediate as the keto tautomer, (E)-2,6-dioxo-6-phenyl-hex-3-enoate. This keto tautomer did not accumulate in either the H265A or the S112A/H265A double variants, indicating that His-265 catalyzes tautomerization. Consistent with this role, the wild type and S112A enzymes catalyzed tautomerization of the product HPD, whereas H265A variants did not. This study thus identifies a keto intermediate, and demonstrates that the catalytic triad histidine catalyzes the tautomerization half-reaction, expanding the role of this residue from its purely hydrolytic function in other serine hydrolases. Finally, the S112A:HOPDA crystal structure is more consistent with hydrolysis occurring via an acyl-enzyme intermediate than a gem-diol intermediate as solvent molecules have poor access to C6, and the closest ordered water is 7 A away.


  • Organizational Affiliation
    • Department of Biochemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.

Macromolecule Content 

  • Total Structure Weight: 32.39 kDa 
  • Atom Count: 2,388 
  • Modeled Residue Count: 283 
  • Deposited Residue Count: 286 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase286Paraburkholderia xenovoransMutation(s): 1 
Gene Names: bphD
EC: 3.7.1 (PDB Primary Data), 3.7.1.8 (UniProt)
UniProt
Find proteins for P47229 (Paraburkholderia xenovorans (strain LB400))
Explore P47229 
Go to UniProtKB:  P47229
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47229
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free:  0.203 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.808α = 90
b = 116.808β = 90
c = 87.589γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-30
    Changes: Data collection, Refinement description