3A8R

The structure of the N-terminal regulatory domain of a plant NADPH oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structure of the N-terminal regulatory domain of a plant NADPH oxidase and its functional implications

Oda, T.Hashimoto, H.Kuwabara, N.Akashi, S.Hayashi, K.Kojima, C.Wong, H.L.Kawasaki, T.Shimamoto, K.Sato, M.Shimizu, T.

(2010) J Biol Chem 285: 1435-1445

  • DOI: https://doi.org/10.1074/jbc.M109.058909
  • Primary Citation of Related Structures:  
    3A8R

  • PubMed Abstract: 

    Plant NADPH oxidases (Rboh, for respiratory burst oxidase homolog) produce reactive oxygen species that are key regulators of various cellular events including plant innate immunity. Rbohs possess a highly conserved cytoplasmic N-terminal region containing two EF-hand motifs that regulate Rboh activity. Rice (Oryza sativa) RbohB (OsRbohB) is regulated by the direct binding of a small GTPase (Rac1) to this regulatory region as well as by Ca(2+) binding to the EF-hands. Here, we present the atomic structure of the N-terminal region of OsRbohB. The structure reveals that OsRbohB forms a unique dimer stabilized by swapping the EF-hand motifs. We identified two additional EF-hand-like motifs that were not predicted from sequence data so far. These EF-hand-like motifs together with the swapped EF-hands form a structure similar to that found in calcineurin B. We observed conformational changes mediated by Ca(2+) binding to only one EF-hand. Structure-based in vitro pulldown assays and NMR titration experiments defined the OsRac1 binding interface within the coiled-coil region created by swapping the EF-hands. In addition, we demonstrate a direct intramolecular interaction between the N and C terminus, and that the complete N-terminal cytoplasmic region is required for this interaction. The structural features and intramolecular interactions characterized here might be common elements shared by Rbohs that contribute to the regulation of reactive oxygen species production.


  • Organizational Affiliation

    Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein
A, B
179Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: B1164G11.26Os01g0360200OsJ_01746
UniProt
Find proteins for Q5ZAJ0 (Oryza sativa subsp. japonica)
Explore Q5ZAJ0 
Go to UniProtKB:  Q5ZAJ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZAJ0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.418α = 90
b = 72.162β = 90
c = 118.902γ = 90
Software Package:
Software NamePurpose
beamdata collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2014-12-17
    Changes: Other
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations