Crystal structure of the Au3+ complex of AphA class B acid phosphatase/phosphotransferase from E. coli at 1.69 A resolution

Experimental Data Snapshot

  • Resolution: 1.69 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

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This is version 1.4 of the entry. See complete history


The first structure of a bacterial class B Acid phosphatase reveals further structural heterogeneity among phosphatases of the haloacid dehalogenase fold.

Calderone, V.Forleo, C.Benvenuti, M.Thaller, M.C.Rossolini, G.M.Mangani, S.

(2004) J Mol Biol 335: 761-773

  • DOI: https://doi.org/10.1016/j.jmb.2003.10.050
  • Primary Citation of Related Structures:  
    1N8N, 1N9K

  • PubMed Abstract: 

    AphA is a periplasmic acid phosphatase of Escherichia coli belonging to class B bacterial phosphatases, which is part of the DDDD superfamily of phosphohydrolases. The crystal structure of AphA has been determined at 2.2A and its resolution extended to 1.7A on an AuCl(3) derivative. This represents the first crystal structure of a class B bacterial phosphatase. Despite the lack of sequence homology, the AphA structure reveals a haloacid dehalogenase-like fold. This finding suggests that this fold could be conserved among members of the DDDD superfamily of phosphohydrolases. The active enzyme is a homotetramer built by using an extended N-terminal arm intertwining the four monomers. The active site of the native enzyme, as prepared, hosts a magnesium ion, which can be replaced by other metal ions. The structure explains the non-specific behaviour of AphA towards substrates, while a structure-based alignment with other phosphatases provides clues about the catalytic mechanism.

  • Organizational Affiliation

    Dipartimento di Chimica, Università di Siena, Via Aldo Moro, I-53100 Siena, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Class B acid phosphatase212Escherichia coliMutation(s): 0 
Gene Names: APHA
Find proteins for P0AE22 (Escherichia coli (strain K12))
Explore P0AE22 
Go to UniProtKB:  P0AE22
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AE22
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on AU3

Download Ideal Coordinates CCD File 
B [auth A]GOLD 3+ ION
Experimental Data & Validation

Experimental Data

  • Resolution: 1.69 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.279α = 90
b = 92.457β = 90
c = 138.182γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-03
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description