3ET5

Structure of Recombinant Haemophilus Influenzae E(P4) Acid Phosphatase Complexed with tungstate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of Recombinant Haemophilus Influenzae E (P4) Acid Phosphatase Reveals a New Member of the Haloacid Dehalogenase Superfamily.

Felts, R.L.Ou, Z.Reilly, T.J.Tanner, J.J.

(2007) Biochemistry 46: 11110

  • DOI: https://doi.org/10.1021/bi701016m
  • Primary Citation of Related Structures:  
    3ET4, 3ET5

  • PubMed Abstract: 

    Lipoprotein e (P4) from Haemophilus influenzae belongs to the "DDDD" superfamily of phosphohydrolases and is the prototype of class C nonspecific acid phosphatases. P4 is also a component of a H. influenzae vaccine. We report the crystal structures of recombinant P4 in the ligand-free and tungstate-inhibited forms, which are the first structures of a class C phosphatase. P4 has a two-domain architecture consisting of a core alpha/beta domain and a smaller alpha domain. The core domain features a five-stranded beta-sheet flanked by helices on both sides that is reminiscent of the haloacid dehalogenase superfamily. The alpha domain appears to be unique and plays roles in substrate binding and dimerization. The active site is solvent accessible and located in a cleft between the two domains. The structure shows that P4 is a metalloenzyme and that magnesium is the most likely metal ion in the crystalline recombinant enzyme. The ligands of the metal ion are the carboxyl groups of the first and third Asp residues of the DDDD motif, the backbone carbonyl of the second Asp of the DDDD motif, and two water molecules. The structure of the tungstate-bound enzyme suggests that Asp64 is the nucleophile that attacks the substrate P atom. Dimerization appears to be important for catalysis because intersubunit contacts stabilize the active site. Analysis of the structural context of mutations engineered for vaccine studies shows that the most promising mutations are located in the dimer interface. This observation suggests a structure-based vaccine design strategy in which the dimer interface is disrupted in order to expose epitopes that are buried in dimeric P4.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein P4, NADP phosphatase255Haemophilus influenzae 86-028NPMutation(s): 0 
Gene Names: helNTHI0816
EC: 3.1.3.2
UniProt
Find proteins for Q4QMM5 (Haemophilus influenzae (strain 86-028NP))
Explore Q4QMM5 
Go to UniProtKB:  Q4QMM5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4QMM5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.848α = 90
b = 65.848β = 90
c = 101.893γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2008-10-14 
  • Deposition Author(s): Tanner, J.J.
  • This entry supersedes: 2HLL

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations