3CZ4

Native AphA class B acid phosphatase/phosphotransferase from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the catalytic mechanism of the bacterial class B phosphatase AphA belonging to the DDDD superfamily of phosphohydrolases.

Leone, R.Cappelletti, E.Benvenuti, M.Lentini, G.Thaller, M.C.Mangani, S.

(2008) J.Mol.Biol. 384: 478-488

  • DOI: 10.1016/j.jmb.2008.09.050

  • PubMed Abstract: 
  • AphA is a magnesium-dependent, bacterial class B acid phosphatase that catalyzes the hydrolysis of a variety of phosphoester substrates and belongs to the DDDD superfamily of phosphohydrolases. The recently reported crystal structure of AphA from Esc ...

    AphA is a magnesium-dependent, bacterial class B acid phosphatase that catalyzes the hydrolysis of a variety of phosphoester substrates and belongs to the DDDD superfamily of phosphohydrolases. The recently reported crystal structure of AphA from Escherichia coli has revealed the quaternary structure of the enzyme together with hints about its catalytic mechanism. The present work reports the crystal structures of AphA from E. coli in complex with substrate, transition-state, and intermediate analogues. The structures provide new insights into the mechanism of the enzyme and allow a revision of some aspects of the previously proposed mechanism that have broader implications for all the phosphatases of the DDDD superfamily.


    Related Citations: 
    • A Structure Based Proposal for the Catalytic Mechanism of the Bacterial Acid Phosphatase AphA belonging to the DDDD Superfamily of Phosphohydrolases
      Calderone, V.,Forleo, C.,Benvenuti, M.,Thaller, M.C.,Rossolini, G.M.,Mangani, S.
      (2006) J.Mol.Biol. 355: 708


    Organizational Affiliation

    Dipartimento di Chimica, Università di Siena, Via Aldo Moro 2, I-53100 Siena, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Class B acid phosphatase
A
212Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: aphA (napA, yjbP)
EC: 3.1.3.2
Find proteins for P0AE22 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AE22
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 49.294α = 90.00
b = 92.775β = 90.00
c = 137.600γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
MOSFLMdata reduction
SCALAdata scaling
ADSCdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance