1MKY

Structural Analysis of the Domain Interactions in Der, a Switch Protein Containing Two GTPase Domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Domain Arrangement of Der, a Switch Protein Containing Two GTPase Domains

Robinson, V.L.Hwang, J.Fox, E.Inouye, M.Stock, A.M.

(2002) Structure 10: 1649-1658


  • PubMed Abstract: 
  • The EngA subfamily of essential bacterial GTPases has a unique domain structure consisting of two adjacent GTPase domains (GD1 and GD2) and a C-terminal domain. The structure of Thermotoga maritima Der bound to GDP determined at 1.9 A resolution reve ...

    The EngA subfamily of essential bacterial GTPases has a unique domain structure consisting of two adjacent GTPase domains (GD1 and GD2) and a C-terminal domain. The structure of Thermotoga maritima Der bound to GDP determined at 1.9 A resolution reveals a novel domain arrangement in which the GTPase domains pack at either side of the C-terminal domain. Unexpectedly, the C-terminal domain resembles a KH domain, missing the distinctive RNA recognition elements. Conserved motifs of the nucleotide binding site of GD1 are integral parts of the GD1-KH domain interface, suggesting the interactions between these two domains are directly influenced by the GTP/GDP cycling of the protein. In contrast, the GD2-KH domain interface is distal to the GDP binding site of GD2.


    Related Citations: 
    • An essential GTPase, der, containing double GTP-binding domains from Escherichia coli and Thermotoga maritima.
      Hwang, J.,Inouye, M.
      (2001) J.Biol.Chem. 276: 31415


    Organizational Affiliation

    Howard Hughes Medical Institute and Center for Advanced Biotechnology and Medicine, 679 Hoes Lane, Piscataway, NJ 08854, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable GTP-binding protein engA
A
439Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Gene Names: der (engA)
Find proteins for Q9X1F8 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9X1F8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.137α = 90.00
b = 77.994β = 90.00
c = 96.597γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-14
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2015-02-04
    Type: Database references, Other