1EEO

CRYSTAL STRUCTURE OF PROTEIN TYROSINE PHOSPHATASE 1B COMPLEXED WITH ACETYL-E-L-E-F-PTYR-M-D-Y-E-NH2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of plasticity in protein tyrosine phosphatase 1B substrate recognition.

Sarmiento, M.Puius, Y.A.Vetter, S.W.Keng, Y.F.Wu, L.Zhao, Y.Lawrence, D.S.Almo, S.C.Zhang, Z.Y.

(2000) Biochemistry 39: 8171-8179

  • Primary Citation of Related Structures:  1EEN

  • PubMed Abstract: 
  • Protein tyrosine phosphatase 1B (PTP1B) displays a preference for peptides containing acidic as well as aromatic/aliphatic residues immediately NH(2)-terminal to phosphotyrosine. The structure of PTP1B bound with DADEpYL-NH(2) (EGFR(988)(-)(993)) off ...

    Protein tyrosine phosphatase 1B (PTP1B) displays a preference for peptides containing acidic as well as aromatic/aliphatic residues immediately NH(2)-terminal to phosphotyrosine. The structure of PTP1B bound with DADEpYL-NH(2) (EGFR(988)(-)(993)) offers a structural explanation for PTP1B's preference for acidic residues [Jia, Z., Barford, D., Flint, A. J., and Tonks, N. K. (1995) Science 268, 1754-1758]. We report here the crystal structures of PTP1B in complex with Ac-ELEFpYMDYE-NH(2) (PTP1B.Con) and Ac-DAD(Bpa)pYLIPQQG (PTP1B.Bpa) determined to 1.8 and 1.9 A resolution, respectively. A structural analysis of PTP1B.Con and PTP1B.Bpa shows how aromatic/aliphatic residues at the -1 and -3 positions of peptide substrates are accommodated by PTP1B. A comparison of the structures of PTP1B.Con and PTP1B.Bpa with that of PTP1B.EGFR(988)(-)(993) reveals the structural basis for the plasticity of PTP1B substrate recognition. PTP1B is able to bind phosphopeptides by utilizing common interactions involving the aromatic ring and phosphate moiety of phosphotyrosine itself, two conserved hydrogen bonds between the Asp48 carboxylate side chain and the main chain nitrogens of the pTyr and residue 1, and a third between the main chain nitrogen of Arg47 and the main chain carbonyl of residue -2. The ability of PTP1B to accommodate both acidic and hydrophobic residues immediately NH(2)-terminal to pTyr appears to be conferred upon PTP1B by a single residue, Arg47. Depending on the nature of the NH(2)-terminal amino acids, the side chain of Arg47 can adopt one of two different conformations, generating two sets of distinct peptide binding surfaces. When an acidic residue is positioned at position -1, a preference for a second acidic residue is also observed at position -2. However, when a large hydrophobic group occupies position -1, Arg47 adopts a new conformation so that it can participate in hydrophobic interactions with both positions -1 and -3.


    Related Citations: 
    • Molecular Basis of Substrate Specificity of Protein-Tyrosine Phosphatase 1B
      Sarmiento, M.,Zhao, Y.,Gordon, S.J.,Zhang, Z.Y.
      (1998) J.Biol.Chem. 273: 26368
    • Identification of a Second Aryl Phosphate-Binding Site in Protein-Tyrosine Phosphatase 1B: A Paradigm for Inhibitor Design
      Puius, Y.A.,Zhao, Y.,Sullivan, M.,Lawrence, D.S.,Almo, S.C.,Zhang, Z.Y.
      (1997) Proc.Natl.Acad.Sci.USA 94: 13420
    • Assessment of Protein-Tyrosine Phosphatase 1B Specificity Using "Inverse Alanine Scanning"
      Vetter, S.W.,Keng, Y.F.,Lawrence, D.S.,Zhang, Z.Y.
      (2000) J.Biol.Chem. 275: 2265
    • Structural Basis for Phosphotyrosine Peptide Recognition by Protein Tyrosine Phosphatase 1B
      Jia, Z.,Barford, D.,Flint, A.J.,Tonks, N.K.
      (1995) Science 268: 1754
    • Determinants of Substrate Recognition in the Protein Tyrosine Phosphatase, Ptp1
      Zhang, Z.Y.,Walsh, A.B.,Wu, L.,Mcnamara, D.J.,Dobrusin, E.M.,Miller, W.T.
      (1996) J.Biol.Chem. 271: 5386


    Organizational Affiliation

    Departments of Biochemistry and Molecular Pharmacology, The Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN TYROSINE PHOSPHATASE 1B
A
321Homo sapiensGene Names: PTPN1 (PTP1B)
EC: 3.1.3.48
Find proteins for P18031 (Homo sapiens)
Go to Gene View: PTPN1
Go to UniProtKB:  P18031
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ACETYL-E-L-E-F-PTYR-M-D-Y-E-NH2 PEPTIDE
B
11N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
B
NON-POLYMERH2 N

--

PTR
Query on PTR
B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
ACE
Query on ACE
B
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.581α = 90.00
b = 82.050β = 90.00
c = 88.543γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-02-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-07-18
    Type: Derived calculations