4Z9B

Crystal structure of Low Molecular Weight Protein Tyrosine Phosphatase isoform A complexed with benzylphosphonic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structures of the apo form and a complex of human LMW-PTP with a phosphonic acid provide new evidence of a secondary site potentially related to the anchorage of natural substrates.

Fonseca, E.M.Trivella, D.B.Scorsato, V.Dias, M.P.Bazzo, N.L.Mandapati, K.R.de Oliveira, F.L.Ferreira-Halder, C.V.Pilli, R.A.Miranda, P.C.Aparicio, R.

(2015) Bioorg.Med.Chem. 23: 4462-4471

  • DOI: 10.1016/j.bmc.2015.06.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Low molecular weight protein tyrosine phosphatases (LMW-PTP, EC 3.1.3.48) are a family of single-domain enzymes with molecular weight up to 18 kDa, expressed in different tissues and considered attractive pharmacological targets for cancer chemothera ...

    Low molecular weight protein tyrosine phosphatases (LMW-PTP, EC 3.1.3.48) are a family of single-domain enzymes with molecular weight up to 18 kDa, expressed in different tissues and considered attractive pharmacological targets for cancer chemotherapy. Despite this, few LMW-PTP inhibitors have been described to date, and the structural information on LMW-PTP druggable binding sites is scarce. In this study, a small series of phosphonic acids were designed based on a new crystallographic structure of LMW-PTP complexed with benzylsulfonic acid, determined at 2.1Å. In silico docking was used as a tool to interpret the structural and enzyme kinetics data, as well as to design new analogs. From the synthesized series, two compounds were found to act as competitive inhibitors, with inhibition constants of 0.124 and 0.047 mM. We also report the 2.4Å structure of another complex in which LMW-PTP is bound to benzylphosphonic acid, and a structure of apo LMW-PTP determined at 2.3Å resolution. Although no appreciable conformation changes were observed, in the latter structures, amino acid residues from an expression tag were found bound to a hydrophobic region at the protein surface. This regions is neighbored by positively charged residues, adjacent to the active site pocket, suggesting that this region might be not a mere artefact of crystal contacts but an indication of a possible anchoring region for the natural substrate-which is a phosphorylated protein.


    Organizational Affiliation

    Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Low molecular weight phosphotyrosine protein phosphatase
A
164Homo sapiensMutation(s): 0 
Gene Names: ACP1
EC: 3.1.3.48
Find proteins for P24666 (Homo sapiens)
Go to Gene View: ACP1
Go to UniProtKB:  P24666
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B85
Query on B85

Download SDF File 
Download CCD File 
A
benzylphosphonic acid
C7 H9 O3 P
OGBVRMYSNSKIEF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 32.088α = 90.00
b = 54.287β = 90.00
c = 97.468γ = 90.00
Software Package:
Software NamePurpose
APEXdata collection
PHASERphasing
APEXdata scaling
REFMACrefinement
APEXdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research FoundationBrazil2009/51602-5
Sao Paulo Research FoundationBrazil2010/17544-5
Sao Paulo Research FoundationBrazil2011/15792-4
Sao Paulo Research FoundationBrazil2011/03054-9

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-08-05
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2018-03-07
    Type: Data collection
  • Version 1.4: 2019-04-17
    Type: Author supporting evidence, Data collection