4ATY

Crystal structure of a Terephthalate 1,2-cis-dihydrodioldehydrogenase from Burkholderia xenovorans LB400


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Investigating Terephthalate Biodegradation: Structural Characterization of a Putative Decarboxylating Cis-Dihydrodiol Dehydrogenase.

Bains, J.Wulff, J.E.Boulanger, M.J.

(2012) J Mol Biol 423: 284

  • DOI: 10.1016/j.jmb.2012.07.022
  • Primary Citation of Related Structures:  
    4ATY

  • PubMed Abstract: 
  • As a highly coveted precursor molecule, terephthalate (Tph) continues to be used extensively for the production of polyethylene Tph bottles, polyester films, and textile fibers worldwide. Based on its detrimental physiological effects, Tph is now recognized as a serious environmental pollutant ...

    As a highly coveted precursor molecule, terephthalate (Tph) continues to be used extensively for the production of polyethylene Tph bottles, polyester films, and textile fibers worldwide. Based on its detrimental physiological effects, Tph is now recognized as a serious environmental pollutant. While amenable to biodegradation and, in fact, traditionally neutralized by aerobic microbiological processes, our current lack of understanding of the enzymatic degradation of Tph at the molecular level presents a major impediment in the development of robust bioremediation strategies. The biodegradation of Tph proceeds through a single metabolic intermediate (a cis-dihydrodiol), which is subsequently converted to the end product (protocatechuate) by a decarboxylating cis-dihydrodiol dehydrogenase (TphB). Using iodide single-wavelength anomalous dispersion, we report the first structural characterization of TphB to 1.85Å resolution. Contrary to prior speculations, a fluorescent scan unambiguously shows that TphB coordinates Zn(2+) and not Fe(2+). The molecular architecture of TphB provides a rationale to the primary-level divergence observed between TphB and other cis-dihydrodiol dehydrogenases while explaining its intriguingly close evolutionary clustering with non-dihydrodiol dehydrogenases belonging to the isocitrate/isopropylmalate family of enzymes. Sequence and structural analyses reveal a putative substrate-binding pocket proximal to the bound Zn(2+). In silico substrate modeling in this putative binding pocket suggests a mechanistic sequence relying on H291, K295, and Zn(2+) as core mediators of catalytic turnover. Overall, this study reveals novel structural and mechanistic insights into a decarboxylating cis-dihydrodiol dehydrogenase that mediates one of the two catalytic steps in the biodegradation of the environmental pollutant Tph.


    Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 3P6.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TEREPHTHALATE 1,2-CIS-DIHYDRODIOL DEHYDROGENASE A349Paraburkholderia xenovorans LB400Mutation(s): 0 
Gene Names: Bxe_B2750
EC: 1.1.1.262
Find proteins for Q13RP4 (Paraburkholderia xenovorans (strain LB400))
Explore Q13RP4 
Go to UniProtKB:  Q13RP4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BME
Query on BME

Download Ideal Coordinates CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.62α = 90
b = 76.19β = 90
c = 197.48γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2012-10-10
    Changes: Database references
  • Version 1.2: 2015-04-29
    Changes: Data collection