2B8J

Crystal structure of AphA class B acid phosphatase/phosphotransferase ternary complex with adenosine and phosphate at 2 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

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: 708-721

  • DOI: https://doi.org/10.1016/j.jmb.2005.10.068
  • Primary Citation of Related Structures:  
    2B82, 2B8J

  • PubMed Abstract: 

    The Escherichia coli gene aphA codes for a periplasmic acid phosphatase called AphA, belonging to class B bacterial phosphatases, which is part of the DDDD superfamily of phosphohydrolases. After our first report about its crystal structure, we have started a series of crystallographic studies aimed at understanding of the catalytic mechanism of the enzyme. Here, we report three crystal structures of the AphA enzyme in complex with the hydrolysis products of nucleoside monophosphate substrates and a fourth with a proposed intermediate analogue that appears to be covalently bound to the enzyme. Comparison with the native enzyme structure and with the available X-ray structures of different phosphatases provides clues about the enzyme chemistry and allows us to propose a catalytic mechanism for AphA, and to discuss it with respect to the mechanism of other bacterial and human phosphatases.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
class B acid phosphatase
A, B
211Escherichia coliMutation(s): 0 
Gene Names: aphAnapA
EC: 3.1.3.2
UniProt
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
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADN
Query on ADN

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I [auth B]ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
SPM
Query on SPM

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D [auth A]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
AU3
Query on AU3

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G [auth A]GOLD 3+ ION
Au
CBMIPXHVOVTTTL-UHFFFAOYSA-N
AU
Query on AU

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F [auth A]GOLD ION
Au
ZBKIUFWVEIBQRT-UHFFFAOYSA-N
PO4
Query on PO4

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E [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
Query on MG

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C [auth A],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.966α = 90
b = 66.544β = 124.02
c = 91.544γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description