3IAE

Structure of benzaldehyde lyase A28S mutant with benzoylphosphonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Active-site engineering of benzaldehyde lyase shows that a point mutation can confer both new reactivity and susceptibility to mechanism-based inhibition.

Brandt, G.S.Kneen, M.M.Petsko, G.A.Ringe, D.McLeish, M.J.

(2010) J.Am.Chem.Soc. 132: 438-439

  • DOI: 10.1021/ja907064w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Benzaldehyde lyase (BAL) from Pseudomonas putida is a thiamin diphosphate (ThDP)-dependent enzyme that catalyzes the breakdown of (R)-benzoin. Here we report that a point mutant, BAL A28S, not only catalyzes the decarboxylation of benzoylformate but, ...

    Benzaldehyde lyase (BAL) from Pseudomonas putida is a thiamin diphosphate (ThDP)-dependent enzyme that catalyzes the breakdown of (R)-benzoin. Here we report that a point mutant, BAL A28S, not only catalyzes the decarboxylation of benzoylformate but, like benzoylformate decarboxylase (BFDC), is also inactivated by the benzoylformate analogues methyl benzoylphosphonate (MBP) and benzoylphosphonate (BP). The latter has no effect on wild-type BAL, and the inactivation of the A28S variant is shown to result from phosphorylation of the newly introduced serine residue. This lends support to the proposal that an appropriately placed nucleophile facilitates the expulsion of carbon dioxide from the active site in many ThDP-dependent decarboxylases.


    Organizational Affiliation

    Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Benzaldehyde lyase
A, B
570Pseudomonas fluorescensMutation(s): 1 
Gene Names: bznB
Find proteins for Q9F4L3 (Pseudomonas fluorescens)
Go to UniProtKB:  Q9F4L3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D7K
Query on D7K

Download SDF File 
Download CCD File 
A, B
3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(S)-hydroxy[(R)-hydroxy(methoxy)phosphoryl]phenylmethyl}-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium
C20 H28 N4 O11 P3 S
NEEQBMRCDKRNBV-FQEVSTJZSA-O
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D7KKi: 130000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.204 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 150.856α = 90.00
b = 150.856β = 90.00
c = 97.240γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
REFMACrefinement
locallydata collection
MOLREPphasing
HKL-2000data reduction
DENZOdata reduction
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description