Novel protein and Mg2+ configurations in the Mg2+GDP complex of the SRP GTPase ffh

Proteins. 2004 Feb 1;54(2):222-30. doi: 10.1002/prot.10598.


Ffh is the signal sequence recognition and targeting subunit of the prokaryotic signal recognition particle (SRP). Previous structural studies of the NG GTPase domain of Ffh demonstrated magnesium-dependent and magnesium-independent binding conformations for GDP and GMPPNP that are believed to reflect novel mechanisms for exchange and activation in this member of the GTPase superfamily. The current study of the NG GTPase bound to Mg(2+)GDP reveals two new binding conformations-in the first the magnesium interactions are similar to those seen previously, however, the protein undergoes a conformational change that brings a conserved aspartate into its second coordination sphere. In the second, the protein conformation is similar to that seen previously, but the magnesium coordination sphere is disrupted so that only five oxygen ligands are present. The loss of the coordinating water molecule, at the position that would be occupied by the oxygen of the gamma-phosphate of GTP, is consistent with that position being privileged for exchange during phosphate release. The available structures of the GDP-bound protein provide a series of structural snapshots that illuminate steps along the pathway of GDP release following GTP hydrolysis.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Motifs
  • Apoproteins / chemistry
  • Apoproteins / metabolism
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Crystallography, X-Ray
  • GTP Phosphohydrolases / chemistry*
  • GTP Phosphohydrolases / metabolism*
  • Guanosine Diphosphate / metabolism*
  • Guanosine Triphosphate / metabolism
  • Guanylyl Imidodiphosphate / metabolism
  • Hydrolysis
  • Ligands
  • Magnesium / metabolism*
  • Models, Molecular
  • Oxygen / metabolism
  • Protein Conformation
  • Signal Recognition Particle / chemistry*
  • Signal Recognition Particle / metabolism*
  • Thermus / chemistry
  • Thermus / enzymology


  • Apoproteins
  • Bacterial Proteins
  • Ligands
  • Signal Recognition Particle
  • Guanosine Diphosphate
  • Guanylyl Imidodiphosphate
  • Guanosine Triphosphate
  • GTP Phosphohydrolases
  • Magnesium
  • Oxygen

Associated data

  • PDB/1O87