3SF0

Structure of Recombinant Haemophilus Influenzae e(P4) Acid Phosphatase mutant D64N complexed with 5'AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of the inhibition of class C acid phosphatases by adenosine 5'-phosphorothioate.

Singh, H.Reilly, T.J.Tanner, J.J.

(2011) Febs J. 278: 4374-4381

  • DOI: 10.1111/j.1742-4658.2011.08360.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The inhibition of phosphatases by adenosine 5'-phosphorothioate (AMPS) was first reported in the late 1960s; however, the structural basis for the inhibition has remained unknown. Here, it is shown that AMPS is a submicromolar inhibitor of class C ac ...

    The inhibition of phosphatases by adenosine 5'-phosphorothioate (AMPS) was first reported in the late 1960s; however, the structural basis for the inhibition has remained unknown. Here, it is shown that AMPS is a submicromolar inhibitor of class C acid phosphatases, a group of bacterial outer membrane enzymes belonging to the haloacid dehalogenase structural superfamily. Furthermore, the 1.35-Å resolution crystal structure of the inhibited recombinant Haemophilus influenzae class C acid phosphatase was determined; this is the first structure of a phosphatase complexed with AMPS. The conformation of AMPS is identical to that of the substrate 5'-AMP, except that steric factors force a rotation of the thiophosphoryl out of the normal phosphoryl-binding pocket. This conformation is catalytically nonproductive, because the P atom is not positioned optimally for nucleophilic attack by Asp64, and the O atom of the scissile O-P bond is too far from the Asp (Asp66) that protonates the leaving group. The structure of 5'-AMP complexed with the Asp64→Asn mutant enzyme was also determined at 1.35-Å resolution. This mutation induces the substrate to adopt the same nonproductive binding mode that is observed in the AMPS complex. In this case, electrostatic considerations, rather than steric factors, underlie the movement of the phosphoryl. The structures not only provide an explanation for the inhibition by AMPS, but also highlight the precise steric and electrostatic requirements of phosphoryl recognition by class C acid phosphatases. Moreover, the structure of the Asp64→Asn mutant illustrates how a seemingly innocuous mutation can cause an unexpected structural change.


    Organizational Affiliation

    Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipoprotein E
A
262Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)Mutation(s): 1 
Gene Names: hel (ompP4)
Find proteins for P26093 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Go to UniProtKB:  P26093
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.142 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 97.897α = 90.00
b = 97.897β = 90.00
c = 107.009γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling
DENZOdata reduction
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-06-12 
  • Released Date: 2011-09-28 
  • Deposition Author(s): Singh, H.

Revision History 

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2012-01-11
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Advisory, Refinement description