2IOF

Crystal structure of phosphonoacetaldehyde hydrolase with sodium borohydride-reduced substrate intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Diversification of function in the haloacid dehalogenase enzyme superfamily: The role of the cap domain in hydrolytic phosphoruscarbon bond cleavage.

Lahiri, S.D.Zhang, G.Dunaway-Mariano, D.Allen, K.N.

(2006) Bioorg.Chem. 34: 394-409

  • DOI: 10.1016/j.bioorg.2006.09.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phosphonatase functions in the 2-aminoethylphosphonate (AEP) degradation pathway of bacteria, catalyzing the hydrolysis of the C-P bond in phosphonoacetaldehyde (Pald) via formation of a bi-covalent Lys53ethylenamine/Asp12 aspartylphosphate intermedi ...

    Phosphonatase functions in the 2-aminoethylphosphonate (AEP) degradation pathway of bacteria, catalyzing the hydrolysis of the C-P bond in phosphonoacetaldehyde (Pald) via formation of a bi-covalent Lys53ethylenamine/Asp12 aspartylphosphate intermediate. Because phosphonatase is a member of the haloacid dehalogenase superfamily, a family predominantly comprised of phosphatases, the question arises as to how this new catalytic activity evolved. The source of general acid-base catalysis for Schiff-base formation and aspartylphosphate hydrolysis was probed using pH-rate profile analysis of active-site mutants and X-ray crystallographic analysis of modified forms of the enzyme. The 2.9 A X-ray crystal structure of the mutant Lys53Arg complexed with Mg2+ and phosphate shows that the equilibrium between the open and the closed conformation is disrupted, favoring the open conformation. Thus, proton dissociation from the cap domain Lys53 is required for cap domain-core domain closure. The likely recipient of the Lys53 proton is a water-His56 pair that serves to relay the proton to the carbonyl oxygen of the phosphonoacetaldehyde (Pald) substrate upon addition of the Lys53. The pH-rate profile analysis of active-site mutants was carried out to test this proposal. The proximal core domain residues Cys22 and Tyr128 were ruled out, and the role of cap domain His56 was supported by the results. The X-ray crystallographic structure of wild-type phosphonatase reduced with NaBH4 in the presence of Pald was determined at 2.4A resolution to reveal N epsilon-ethyl-Lys53 juxtaposed with a sulfate ligand bound in the phosphate site. The position of the C2 of the N-ethyl group in this structure is consistent with the hypothesis that the cap domain N epsilon-ethylenamine-Lys53 functions as a general base in the hydrolysis of the aspartylphosphate bi-covalent enzyme intermediate. Because the enzyme residues proposed to play a key role in P-C bond cleavage are localized on the cap domain, this domain appears to have evolved to support the diversification of the HAD phosphatase core domain for catalysis of hydrolytic P-C bond cleavage.


    Organizational Affiliation

    Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118-2394, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphonoacetaldehyde hydrolase
A
267Bacillus cereusMutation(s): 0 
Gene Names: phnX
EC: 3.11.1.1
Find proteins for O31156 (Bacillus cereus)
Go to UniProtKB:  O31156
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phosphonoacetaldehyde hydrolase
K
267Bacillus cereusMutation(s): 0 
Gene Names: phnX
EC: 3.11.1.1
Find proteins for O31156 (Bacillus cereus)
Go to UniProtKB:  O31156
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, K
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, K
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LDH
Query on LDH
K
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.231 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 159.820α = 90.00
b = 64.020β = 123.52
c = 98.330γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
CNSrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-07-24
    Type: Data collection, Derived calculations, Refinement description