5NP5

Abl2 SH3 pTyr116/161


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the tyrosine phosphorylation-mediated inhibition of SH3 domain-ligand interactions.

Mero, B.Radnai, L.Gogl, G.Toke, O.Leveles, I.Koprivanacz, K.Szeder, B.Dulk, M.Kudlik, G.Vas, V.Cserkaszky, A.Sipeki, S.Nyitray, L.Vertessy, B.G.Buday, L.

(2019) J Biol Chem 294: 4608-4620

  • DOI: 10.1074/jbc.RA118.004732
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Src homology 3 (SH3) domains bind proline-rich linear motifs in eukaryotes. By mediating inter- and intramolecular interactions, they regulate the functions of many proteins involved in a wide variety of signal transduction pathways. Phosphorylation ...

    Src homology 3 (SH3) domains bind proline-rich linear motifs in eukaryotes. By mediating inter- and intramolecular interactions, they regulate the functions of many proteins involved in a wide variety of signal transduction pathways. Phosphorylation at different tyrosine residues in SH3 domains has been reported previously. In several cases, the functional consequences have also been investigated. However, a full understanding of the effects of tyrosine phosphorylation on the ligand interactions and cellular functions of SH3 domains requires detailed structural, atomic-resolution studies along with biochemical and biophysical analyses. Here, we present the first crystal structures of tyrosine-phosphorylated human SH3 domains derived from the Abelson-family kinases ABL1 and ABL2 at 1.6 and 1.4 Å resolutions, respectively. The structures revealed that simultaneous phosphorylation of Tyr 89 and Tyr 134 in ABL1 or the homologous residues Tyr 116 and Tyr 161 in ABL2 induces only minor structural perturbations. Instead, the phosphate groups sterically blocked the ligand-binding grooves, thereby strongly inhibiting the interaction with proline-rich peptide ligands. Although some crystal contact surfaces involving phosphotyrosines suggested the possibility of tyrosine phosphorylation-induced dimerization, we excluded this possibility by using small-angle X-ray scattering (SAXS), dynamic light scattering (DLS), and NMR relaxation analyses. Extensive analysis of relevant databases and literature revealed not only that the residues phosphorylated in our model systems are well-conserved in other human SH3 domains, but that the corresponding tyrosines are known phosphorylation sites in vivo in many cases. We conclude that tyrosine phosphorylation might be a mechanism involved in the regulation of the human SH3 interactome.


    Organizational Affiliation

    the Department of Medical Chemistry, Semmelweis University Medical School, Tűzoltó u. 37-47, Budapest H-1094, Hungary.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Abelson tyrosine-protein kinase 2A, B61Homo sapiensMutation(s): 0 
Gene Names: ABL2ABLLARG
EC: 2.7.10.2
Find proteins for P42684 (Homo sapiens)
Explore P42684 
Go to UniProtKB:  P42684
NIH Common Fund Data Resources
PHAROS  P42684
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A,BL-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 22.51α = 90
b = 45.91β = 89.74
c = 45.77γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2019-01-30
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Database references