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Solution structure of the RWD domain of mouse GCN2


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations, structures with the lowest energy, target function 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of the RWD domain of the mouse GCN2 protein.

Nameki, N.Yoneyama, M.Koshiba, S.Tochio, N.Inoue, M.Seki, E.Matsuda, T.Tomo, Y.Harada, T.Saito, K.Kobayashi, N.Yabuki, T.Aoki, M.Nunokawa, E.Matsuda, N.Sakagami, N.Terada, T.Shirouzu, M.Yoshida, M.Hirota, H.Osanai, T.Tanaka, A.Arakawa, T.Carninci, P.Kawai, J.Hayashizaki, Y.Kinoshita, K.Guntert, P.Kigawa, T.Yokoyama, S.

(2004) Protein Sci. 13: 2089-2100

  • DOI: 10.1110/ps.04751804

  • PubMed Abstract: 
  • GCN2 is the alpha-subunit of the only translation initiation factor (eIF2alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major R ...

    GCN2 is the alpha-subunit of the only translation initiation factor (eIF2alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. In this study, we determined the solution structure of the mouse GCN2 RWD domain using NMR spectroscopy. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices, with an alphabetabetabetabetaalphaalpha topology. A characteristic YPXXXP motif, which always occurs in RWD domains, forms a stable loop including three consecutive beta-turns that overlap with each other by two residues (triple beta-turn). As putative binding sites with GCN1, a structure-based alignment allowed the identification of several surface residues in alpha-helix 3 that are characteristic of the GCN2 RWD domains. Despite the apparent absence of sequence similarity, the RWD structure significantly resembles that of ubiquitin-conjugating enzymes (E2s), with most of the structural differences in the region connecting beta-strand 4 and alpha-helix 3. The structural architecture, including the triple beta-turn, is fundamentally common among various RWD domains and E2s, but most of the surface residues on the structure vary. Thus, it appears that the RWD domain is a novel structural domain for protein-binding that plays specific roles in individual RWD-containing proteins.


    Organizational Affiliation

    RIKEN Genomic Sciences Center, Tsurumi, Yokohama, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GCN2 eIF2alpha kinase
A
137Mus musculusMutation(s): 0 
Gene Names: Eif2ak4 (Gcn2, Kiaa1338)
Find proteins for Q9QZ05 (Mus musculus)
Go to UniProtKB:  Q9QZ05
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations, structures with the lowest energy, target function 
  • Olderado: 1UKX Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance