4RJ9

Structure of a plant specific C2 domain protein, OsGAP1 from rice


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Site-directed Mutagenesis Shows the Significance of Interactions with Phospholipids and the G-protein OsYchF1 for the Physiological Functions of the Rice GTPase-activating Protein 1 (OsGAP1).

Yung, Y.L.Cheung, M.Y.Miao, R.Fong, Y.H.Li, K.P.Yu, M.H.Chye, M.L.Wong, K.B.Lam, H.M.

(2015) J Biol Chem 290: 23984-23996

  • DOI: 10.1074/jbc.M115.655639
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The C2 domain is one of the most diverse phospholipid-binding domains mediating cellular signaling. One group of C2-domain proteins are plant-specific and are characterized by their small sizes and simple structures. We have previously reported that ...

    The C2 domain is one of the most diverse phospholipid-binding domains mediating cellular signaling. One group of C2-domain proteins are plant-specific and are characterized by their small sizes and simple structures. We have previously reported that a member of this group, OsGAP1, is able to alleviate salt stress and stimulate defense responses, and bind to both phospholipids and an unconventional G-protein, OsYchF1. Here we solved the crystal structure of OsGAP1 to a resolution of 1.63 Å. Using site-directed mutagenesis, we successfully differentiated between the clusters of surface residues that are required for binding to phospholipids versus OsYchF1, which, in turn, is critical for its role in stimulating defense responses. On the other hand, the ability to alleviate salt stress by OsGAP1 is dependent only on its ability to bind OsYchF1 and is independent of its phospholipid-binding activity.


    Organizational Affiliation

    From the School of Life Sciences, Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, and honming@cuhk.edu.hk.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C2 domain-containing protein-like
A
165Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: Os02g0327000OsGAP1OSJNBb0042G06.10OsJ_06508P0476C12.36GAP1GPBP1LOC_Os02g22130
EC: 6.5.1.1
Find proteins for Q6YWF1 (Oryza sativa subsp. japonica)
Go to UniProtKB:  Q6YWF1
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.19α = 90
b = 166.75β = 90
c = 60.73γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASESphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-09-02
    Changes: Database references
  • Version 1.2: 2015-10-21
    Changes: Database references