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PDBsum entry 2q9c
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protein ligands Protein-protein interface(s) links
Signaling protein PDB id
2q9c

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
304 a.a. *
Ligands
SO4 ×8
GNP
Waters ×358
* Residue conservation analysis
PDB id:
2q9c
Name: Signaling protein
Title: Structure of ftsy:gmppnp with mgcl complex
Structure: Cell division protein ftsy. Chain: a, b. Synonym: ftsy. Engineered: yes
Source: Thermus aquaticus. Organism_taxid: 271. Gene: ftsy. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.20Å     R-factor:   0.203     R-free:   0.274
Authors: C.L.Reyes,R.M.Stroud
Key ref: C.L.Reyes et al. (2007). X-ray structures of the signal recognition particle receptor reveal targeting cycle intermediates. Plos One, 2, e607. PubMed id: 17622352
Date:
12-Jun-07     Release date:   03-Jul-07    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P83749  (FTSY_THEAQ) -  Signal recognition particle receptor FtsY from Thermus aquaticus
Seq:
Struc: 		304 a.a.
304 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.6.5.4  - signal-recognition-particle GTPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: GTP + H2O = GDP + phosphate + H+
GTP
 + H2O
 =
GDP
Bound ligand (Het Group name = GNP)
matches with 81.82% similarity 		+ phosphate
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Plos One 2:e607 (2007)
PubMed id: 17622352  
 
 
X-ray structures of the signal recognition particle receptor reveal targeting cycle intermediates.
C.L.Reyes, E.Rutenber, P.Walter, R.M.Stroud.
 
  ABSTRACT  
 
The signal recognition particle (SRP) and its conjugate receptor (SR) mediate cotranslational targeting of a subclass of proteins destined for secretion to the endoplasmic reticulum membrane in eukaryotes or to the plasma membrane in prokaryotes. Conserved active site residues in the GTPase domains of both SRP and SR mediate discrete conformational changes during formation and dissociation of the SRP.SR complex. Here, we describe structures of the prokaryotic SR, FtsY, as an apo protein and in two different complexes with a non-hydrolysable GTP analog (GMPPNP). These structures reveal intermediate conformations of FtsY containing GMPPNP and explain how the conserved active site residues position the nucleotide into a non-catalytic conformation. The basis for the lower specificity of binding of nucleotide in FtsY prior to heterodimerization with the SRP conjugate Ffh is also shown. We propose that these structural changes represent discrete conformational states assumed by FtsY during targeting complex formation and dissociation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21330537 S.F.Ataide, N.Schmitz, K.Shen, A.Ke, S.O.Shan, J.A.Doudna, and N.Ban (2011).
The crystal structure of the signal recognition particle in complex with its receptor.
  Science, 331, 881-886.
PDB code: 2xxa
20544960 M.Yang, X.Zhang, and K.Han (2010).
Molecular dynamics simulation of SRP GTPases: towards an understanding of the complex formation from equilibrium fluctuations.
  Proteins, 78, 2222-2237.  
20162627 O.Doppelt-Azeroual, F.Delfaud, F.Moriaud, and A.G.de Brevern (2010).
Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins.
  Protein Sci, 19, 847-867.  
18078384 A.J.Driessen, and N.Nouwen (2008).
Protein translocation across the bacterial cytoplasmic membrane.
  Annu Rev Biochem, 77, 643-667.  
18978942 P.F.Egea, H.Tsuruta, G.P.de Leon, J.Napetschnig, P.Walter, and R.M.Stroud (2008).
Structures of the signal recognition particle receptor from the archaeon Pyrococcus furiosus: implications for the targeting step at the membrane.
  PLoS ONE, 3, e3619.
PDB codes: 3dm9 3dmd 3e70
19172744 S.B.Neher, N.Bradshaw, S.N.Floor, J.D.Gross, and P.Walter (2008).
SRP RNA controls a conformational switch regulating the SRP-SRP receptor interaction.
  Nat Struct Mol Biol, 15, 916-923.  
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
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 code is shown on the right.

 

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