PDBsum entry 1o87

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protein ligands metals Protein-protein interface(s) links
Protein transport PDB id
Protein chains
295 a.a. *
FMT ×5
GDP ×2
_MG ×4
Waters ×274
* Residue conservation analysis
PDB id:
Name: Protein transport
Title: A new mggdp complex of the ffh ng domain
Structure: Signal recognition particle protein. Chain: a, b. Fragment: ng gtpase domain, residues 1-296. Synonym: fifty-four homolog, ffh. Engineered: yes
Source: Thermus aquaticus. Organism_taxid: 271. Expressed in: escherichia coli. Expression_system_taxid: 562
2.1Å     R-factor:   0.197     R-free:   0.237
Authors: D.M.Freymann
Key ref:
P.J.Focia et al. (2004). Novel protein and Mg2+ configurations in the Mg2+GDP complex of the SRP GTPase ffh. Proteins, 54, 222-230. PubMed id: 14696184 DOI: 10.1002/prot.10598
25-Nov-02     Release date:   02-Jan-04    
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Protein chains
Pfam   ArchSchema ?
O07347  (SRP54_THEAQ) -  Signal recognition particle protein
430 a.a.
295 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     signal recognition particle   1 term 
  Biological process     SRP-dependent cotranslational protein targeting to membrane   1 term 
  Biochemical function     GTP binding     2 terms  


DOI no: 10.1002/prot.10598 Proteins 54:222-230 (2004)
PubMed id: 14696184  
Novel protein and Mg2+ configurations in the Mg2+GDP complex of the SRP GTPase ffh.
P.J.Focia, H.Alam, T.Lu, U.D.Ramirez, D.M.Freymann.
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.
  Selected figure(s)  
Figure 1.
Figure 1. Ribbon diagram of the nucleotide bound protein. The ribbon diagram of monomer A of the Mg^2+GDP complex of the Ffh NG domain is oriented to view into the active site. The -helical N domain is in light blue, and the G domain is in light green. The motif I P-loop at the center of the G domain interacts with the phosphate groups of GDP (ball-and-stick). Motif II to the left, and motif III to the center right (indicated), interact with the bound magnesium ion through intervening water molecules. The hydrated magnesium ion is shown as a CPK representation. The carboxylate group of Asp248 hydrogen-bonds the guanine base; the carboxylate of Asp135 contributes to the second coordination sphere of the magnesium in monomer A, but is usually found in a different conformation (see text).
Figure 3.
Figure 3. Difference in magnesium ion hydration in monomers A and B. The 2Fo-Fc electron density maps of the hydrated magnesium ions in the active sites of monomers A and B are shown, contoured at 1.0 . In monomer A, each of the coordinating water molecules is clearly defined. In contrast, although three coordinating waters are well defined in monomer B, and the temperature factors of the magnesium ions and coordinating waters are similar, no coordinating water at position 1 (asterisk) is visible in the electron density map. As this position is the site of interaction with the -phosphate oxygen of bound GTP, facile exchange may be functionally significant. The magnesium omit difference map allowed for an identical interpretation. Thr112 and the phosphate groups of the bound GDP are shown in each figure. The map cover radius was 1.1 Å, including the missing water position.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 54, 222-230) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18953414 P.F.Egea, J.Napetschnig, P.Walter, and R.M.Stroud (2008).
Structures of SRP54 and SRP19, the two proteins that organize the ribonucleic core of the signal recognition particle from Pyrococcus furiosus.
  PLoS ONE, 3, e3528.
PDB codes: 3dlu 3dlv 3dm5
18931411 U.D.Ramirez, P.J.Focia, and D.M.Freymann (2008).
Nucleotide-binding flexibility in ultrahigh-resolution structures of the SRP GTPase Ffh.
  Acta Crystallogr D Biol Crystallogr, 64, 1043-1053.
PDB codes: 2c03 2c04
17186523 J.Gawronski-Salerno, J.S.Coon, P.J.Focia, and D.M.Freymann (2007).
X-ray structure of the T. aquaticus FtsY:GDP complex suggests functional roles for the C-terminal helix of the SRP GTPases.
  Proteins, 66, 984-995.
PDB code: 2iyl
17139088 U.D.Ramirez, and D.M.Freymann (2006).
Analysis of protein hydration in ultrahigh-resolution structures of the SRP GTPase Ffh.
  Acta Crystallogr D Biol Crystallogr, 62, 1520-1534.
PDB codes: 2j45 2j46
14726591 P.J.Focia, I.V.Shepotinovskaya, J.A.Seidler, and D.M.Freymann (2004).
Heterodimeric GTPase core of the SRP targeting complex.
  Science, 303, 373-377.
PDB code: 1okk
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.