3NR8

Crystal structure of human SHIP2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for phosphoinositide substrate recognition, catalysis, and membrane interactions in human inositol polyphosphate 5-phosphatases

Tresaugues, L.Silvander, C.Flodin, S.Welin, M.Nyman, T.Graslund, S.Hammarstrom, M.Berglund, H.Nordlund, P.

(2014) Structure 22: 744-755

  • DOI: 10.1016/j.str.2014.01.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • SHIP2, OCRL, and INPP5B belong to inositol polyphosphate 5-phophatase subfamilies involved in insulin regulation and Lowes syndrome. The structural basis for membrane recognition, substrate specificity, and regulation of inositol polyphosphate 5-phop ...

    SHIP2, OCRL, and INPP5B belong to inositol polyphosphate 5-phophatase subfamilies involved in insulin regulation and Lowes syndrome. The structural basis for membrane recognition, substrate specificity, and regulation of inositol polyphosphate 5-phophatases is still poorly understood. We determined the crystal structures of human SHIP2, OCRL, and INPP5B, the latter in complex with phosphoinositide substrate analogs, which revealed a membrane interaction patch likely to assist in sequestering substrates from the lipid bilayer. Residues recognizing the 1-phosphate of the substrates are highly conserved among human family members, suggesting similar substrate binding modes. However, 3- and 4-phosphate recognition varies and determines individual substrate specificity profiles. The high conservation of the environment of the scissile 5-phosphate suggests a common reaction geometry for all members of the human 5-phosphatase family.


    Organizational Affiliation

    Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden. Electronic address: camilla.silvander@sprintbioscience.com.,Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden.,Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden; Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden; Centre for Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, 637551, Singapore. Electronic address: par.nordlund@ki.se.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2
B, A
316Homo sapiensMutation(s): 0 
Gene Names: INPPL1 (SHIP2)
EC: 3.1.3.86
Find proteins for O15357 (Homo sapiens)
Go to Gene View: INPPL1
Go to UniProtKB:  O15357
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.796α = 90.00
b = 61.177β = 91.90
c = 114.320γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
PHASERphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-05-28
    Type: Database references