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PDBsum entry 2cnw

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protein ligands metals Protein-protein interface(s) links
Signal recognition PDB id
2cnw
Jmol
Contents
Protein chains
290 a.a. *
281 a.a. *
260 a.a. *
Ligands
GDP ×6
ALF ×6
5GP ×3
Metals
_MG ×6
Waters ×621
* Residue conservation analysis
PDB id:
2cnw
Name: Signal recognition
Title: Gdpalf4 complex of the srp gtpases ffh and ftsy
Structure: Signal recognition particle protein. Chain: a, b, c. Fragment: ng domain residues 1-293. Synonym: ffh, fifty-four homolog. Engineered: yes. Other_details: gdp, alf4, gmp. Cell division protein ftsy. Chain: d, e, f. Fragment: residues 20-303.
Source: Thermus aquaticus. Organism_taxid: 271. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.39Å     R-factor:   0.186     R-free:   0.253
Authors: P.J.Focia,J.Gawronski-Salerno,J.S.Coon V,D.M.Freymann
Key ref:
P.J.Focia et al. (2006). Structure of a GDP:AlF4 complex of the SRP GTPases Ffh and FtsY, and identification of a peripheral nucleotide interaction site. J Mol Biol, 360, 631-643. PubMed id: 16780874 DOI: 10.1016/j.jmb.2006.05.031
Date:
24-May-06     Release date:   11-Oct-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O07347  (SRP54_THEAQ) -  Signal recognition particle protein
Seq:
Struc:
430 a.a.
290 a.a.
Protein chains
Pfam   ArchSchema ?
P83749  (FTSY_THEAQ) -  Signal recognition particle receptor FtsY
Seq:
Struc:
304 a.a.
281 a.a.
Protein chain
Pfam   ArchSchema ?
P83749  (FTSY_THEAQ) -  Signal recognition particle receptor FtsY
Seq:
Struc:
304 a.a.
260 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   5 terms 
  Biological process     protein targeting to membrane   3 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
DOI no: 10.1016/j.jmb.2006.05.031 J Mol Biol 360:631-643 (2006)
PubMed id: 16780874  
 
 
Structure of a GDP:AlF4 complex of the SRP GTPases Ffh and FtsY, and identification of a peripheral nucleotide interaction site.
P.J.Focia, J.Gawronski-Salerno, J.S.Coon, D.M.Freymann.
 
  ABSTRACT  
 
The signal recognition particle (SRP) GTPases Ffh and FtsY play a central role in co-translational targeting of proteins, assembling in a GTP-dependent manner to generate the SRP targeting complex at the membrane. A suite of residues in FtsY have been identified that are essential for the hydrolysis of GTP that accompanies disengagement. We have argued previously on structural grounds that this region mediates interactions that serve to activate the complex for disengagement and term it the activation region. We report here the structure of a complex of the SRP GTPases formed in the presence of GDP:AlF4. This complex accommodates the putative transition-state analog without undergoing significant change from the structure of the ground-state complex formed in the presence of the GTP analog GMPPCP. However, small shifts that do occur within the shared catalytic chamber may be functionally important. Remarkably, an external nucleotide interaction site was identified at the activation region, revealed by an unexpected contaminating GMP molecule bound adjacent to the catalytic chamber. This site exhibits conserved sequence and structural features that suggest a direct interaction with RNA plays a role in regulating the activity of the SRP targeting complex.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. The external nucleotide-binding site. (a) Omit F[o]–F[c] electron density at the external nucleotide-binding site, contoured at 3 σ (blue) and 7.5 σ (black). The density, located between motifs II and III of FtsY (below, purple) and the closing loop of Ffh (above), enters the water-filled channel that abuts the shared active site chamber,^13 and is close to both active site nucleotides (shown ”ghosted”). (b) Stereo view of the hydrogen bonding interactions between the external GMP molecule and residues and water molecules at the complex interface are shown in an orientation similar to that in (a). Key water molecules are shown as larger spheres and labeled as in Figure 2(c). Ffh residues are highlighted in grey, FtsY residues in purple, and motifs I, II and III are labeled. Phe141 participates in π-π stacking interactions with the purine ring of the GMP molecule (front, center). Figure 4. The external nucleotide-binding site. (a) Omit F[o]–F[c] electron density at the external nucleotide-binding site, contoured at 3 σ (blue) and 7.5 σ (black). The density, located between motifs II and III of FtsY (below, purple) and the closing loop of Ffh (above), enters the water-filled channel that abuts the shared active site chamber,[3]^13 and is close to both active site nucleotides (shown ”ghosted”). (b) Stereo view of the hydrogen bonding interactions between the external GMP molecule and residues and water molecules at the complex interface are shown in an orientation similar to that in (a). Key water molecules are shown as larger spheres and labeled as in [4]Figure 2(c). Ffh residues are highlighted in grey, FtsY residues in purple, and motifs I, II and III are labeled. Phe141 participates in π-π stacking interactions with the purine ring of the GMP molecule (front, center).
Figure 5.
Figure 5. Features of the complex surface. Mutations of FtsY interface residues that affect assembly of the complex, and those that do not affect assembly but affect the subsequent GTPase hydrolysis step,^15 are mapped onto the surface of FtsY (gold, assembly defect; magenta, activity defect). The orientation is looking into the GTPase binding site where bound GTP is drawn as sticks. Activity defect mutations cluster (at the bottom) near the FtsY active center, locating residues that likely contribute to the activation region of the complex. The relative position of the external nucleotide site is indicated with an asterisk (*); however, formation of that binding site requires assembly of the heterodimer. Figure 5. Features of the complex surface. Mutations of FtsY interface residues that affect assembly of the complex, and those that do not affect assembly but affect the subsequent GTPase hydrolysis step,[3]^15 are mapped onto the surface of FtsY (gold, assembly defect; magenta, activity defect). The orientation is looking into the GTPase binding site where bound GTP is drawn as sticks. Activity defect mutations cluster (at the bottom) near the FtsY active center, locating residues that likely contribute to the activation region of the complex. The relative position of the external nucleotide site is indicated with an asterisk (*); however, formation of that binding site requires assembly of the heterodimer.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 360, 631-643) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22056770 G.Bange, N.Kümmerer, P.Grudnik, R.Lindner, G.Petzold, D.Kressler, E.Hurt, K.Wild, and I.Sinning (2011).
Structural basis for the molecular evolution of SRP-GTPase activation by protein.
  Nat Struct Mol Biol, 18, 1376-1380.
PDB code: 3syn
  21465554 M.J.Yang, and X.Zhang (2011).
Molecular dynamics simulations reveal structural coordination of Ffh-FtsY heterodimer toward GTPase activation.
  Proteins, 79, 1774-1785.  
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
21464281 X.Zhang, V.Q.Lam, Y.Mou, T.Kimura, J.Chung, S.Chandrasekar, J.R.Winkler, S.L.Mayo, and S.O.Shan (2011).
Direct visualization reveals dynamics of a transient intermediate during protein assembly.
  Proc Natl Acad Sci U S A, 108, 6450-6455.  
20385832 K.Shen, and S.O.Shan (2010).
Transient tether between the SRP RNA and SRP receptor ensures efficient cargo delivery during cotranslational protein targeting.
  Proc Natl Acad Sci U S A, 107, 7698-7703.  
19558326 P.Grudnik, G.Bange, and I.Sinning (2009).
Protein targeting by the signal recognition particle.
  Biol Chem, 390, 775-782.  
19174514 X.Zhang, C.Schaffitzel, N.Ban, and S.O.Shan (2009).
Multiple conformational switches in a GTPase complex control co-translational protein targeting.
  Proc Natl Acad Sci U S A, 106, 1754-1759.  
18650931 K.Gotthardt, M.Weyand, A.Kortholt, P.J.Van Haastert, and A.Wittinghofer (2008).
Structure of the Roc-COR domain tandem of C. tepidum, a prokaryotic homologue of the human LRRK2 Parkinson kinase.
  EMBO J, 27, 2239-2249.
PDB codes: 3dpt 3dpu
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
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
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.  
18617187 X.Zhang, S.Kung, and S.O.Shan (2008).
Demonstration of a multistep mechanism for assembly of the SRP x SRP receptor complex: implications for the catalytic role of SRP RNA.
  J Mol Biol, 381, 581-593.  
17622352 C.L.Reyes, E.Rutenber, P.Walter, and R.M.Stroud (2007).
X-ray structures of the signal recognition particle receptor reveal targeting cycle intermediates.
  PLoS ONE, 2, e607.
PDB codes: 2q9a 2q9b 2q9c
17164479 F.Y.Siu, R.J.Spanggord, and J.A.Doudna (2007).
SRP RNA provides the physiologically essential GTPase activation function in cotranslational protein targeting.
  RNA, 13, 240-250.  
17184999 J.Gawronski-Salerno, and D.M.Freymann (2007).
Structure of the GMPPNP-stabilized NG domain complex of the SRP GTPases Ffh and FtsY.
  J Struct Biol, 158, 122-128.
PDB code: 2j7p
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
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.