3IAE

Structure of benzaldehyde lyase A28S mutant with benzoylphosphonate

• PDB DOI: https://doi.org/10.2210/pdb3IAE/pdb

• Classification: LYASE
• Organism(s): Pseudomonas fluorescens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-07-13 Released: 2010-03-02 
• Deposition Author(s): Brandt, G.S., Petsko, G.A., Ringe, D., McLeish, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.234 
• R-Value Work: 0.204 
• R-Value Observed: 0.207 

Starting Model: experimental

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

• PubMed: 20030408 
• DOI: https://doi.org/10.1021/ja907064w
• Primary Citation of Related Structures:  
  3IAE, 3IAF


• 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, 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 121.12 kDa 
• Atom Count: 8,450 
• Modelled Residue Count: 1,108 
• Deposited Residue Count: 1,140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzaldehyde lyase	A, B	570	Pseudomonas fluorescens	Mutation(s): 1  Gene Names: bznB EC: 4.1.2.38
UniProt
Find proteins for Q9F4L3 (Pseudomonas fluorescens) Explore Q9F4L3  Go to UniProtKB:  Q9F4L3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D7K	C [auth A], E [auth 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
CA	D [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
D7K	PDBBind:  3IAE	Ki: 1.30e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.234 
• R-Value Work: 0.204 
• R-Value Observed: 0.207 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.856	α = 90
b = 150.856	β = 90
c = 97.24	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
locally	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Brandt, G.S., Petsko, G.A., Ringe, D., McLeish, M.J.

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description