2Y53

Crystal structure of E257Q mutant of the box pathway encoded ALDH from Burkholderia xenovorans LB400

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

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Literature

Elucidating the Reaction Mechanism of the Benzoate Oxidation Pathway Encoded Aldehyde Dehydrogenase from Burkholderia Xenovorans Lb400.

Bains, J., Leon, R., Temke, K.G., Boulanger, M.J.

(2011) Protein Sci 20: 1048

  • DOI: 10.1002/pro.639
  • Primary Citation of Related Structures:  
    2Y51, 2Y52, 2Y53, 2Y5D

  • PubMed Abstract: 

    • Oxidation of cis-3,4-dehydroadipyl-CoA semialdehyde to cis-3,4-dehydroadipyl-CoA by the aldehyde dehydrogenase, ALDH(C) (EC.1.2.1.77), is an essential step in the metabolism of benzoate in Burkholderia xenovorans LB400. In a previous study, we established a structural blueprint for this novel group of ALDH enzymes ...

    Oxidation of cis-3,4-dehydroadipyl-CoA semialdehyde to cis-3,4-dehydroadipyl-CoA by the aldehyde dehydrogenase, ALDH(C) (EC.1.2.1.77), is an essential step in the metabolism of benzoate in Burkholderia xenovorans LB400. In a previous study, we established a structural blueprint for this novel group of ALDH enzymes. Here, we build significantly on this initial work and propose a detailed reaction mechanism for ALDH(C) based on comprehensive structural and functional investigations of active site residues. Kinetic analyses reveal essential roles for C296 as the nucleophile and E257 as the associated general base. Structural analyses of E257Q and C296A variants suggest a dynamic charge repulsion relationship between E257 and C296 that contributes to the inherent flexibility of E257 in the native enzyme, which is further regulated by E496 and E167. A proton relay network anchored by E496 and supported by E167 and K168 serves to reset E257 for the second catalytic step. We also propose that E167, which is unique to ALDH(C) and its homologs, serves a critical role in presenting the catalytic water to the newly reset E257 such that the enzyme can proceed with deacylation and product release. Collectively, the reaction mechanism proposed for ALDH(C) promotes a greater understanding of these novel ALDH enzymes, the ALDH super-family in general, and benzoate degradation in B. xenovorans LB400.

    Organizational Affiliation: 

    Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W3P6, Canada.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALDEHYDE DEHYDROGENASE (BOX PATHWAY)A, B534Paraburkholderia xenovorans LB400Mutation(s): 1 
Gene Names: Bxe_A1420
EC: 1.2.1
UniProt
Find proteins for Q13WK4 (Paraburkholderia xenovorans (strain LB400))
Explore Q13WK4 
Go to UniProtKB:  Q13WK4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13WK4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]		NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
H [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.24α = 111.22
b = 67.81β = 90.45
c = 77.51γ = 113.51
Software Package:
Software NamePurpose
REFMACrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-01
    Type: Initial release
  • Version 1.1: 2015-10-07
    Changes: Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Version format compliance