Limits...
Structures of the signal recognition particle receptor from the archaeon Pyrococcus furiosus: implications for the targeting step at the membrane.

Egea PF, Tsuruta H, de Leon GP, Napetschnig J, Walter P, Stroud RM - PLoS ONE (2008)

Bottom Line: The basic charges on the surface of this helix are likely to regulate interactions at the membrane.Small angle X-ray scattering and analytical ultracentrifugation indicate that the crystal structure of Pfu-FtsY correlates well with the average conformation in solution.Based on previous structures of two sub-complexes, we propose a model of the core of archeal and eukaryotic SRP*SR targeting complexes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA. pascal@msg.ucsf.edu

ABSTRACT
In all organisms, a ribonucleoprotein called the signal recognition particle (SRP) and its receptor (SR) target nascent proteins from the ribosome to the translocon for secretion or membrane insertion. We present the first X-ray structures of an archeal FtsY, the receptor from the hyper-thermophile Pyrococcus furiosus (Pfu), in its free and GDP*magnesium-bound forms. The highly charged N-terminal domain of Pfu-FtsY is distinguished by a long N-terminal helix. The basic charges on the surface of this helix are likely to regulate interactions at the membrane. A peripheral GDP bound near a regulatory motif could indicate a site of interaction between the receptor and ribosomal or SRP RNAs. Small angle X-ray scattering and analytical ultracentrifugation indicate that the crystal structure of Pfu-FtsY correlates well with the average conformation in solution. Based on previous structures of two sub-complexes, we propose a model of the core of archeal and eukaryotic SRP*SR targeting complexes.

Show MeSH

Related in: MedlinePlus

Model of domain rearrangement in Pfu-FtsY upon its interaction with SRP54.(A) The overall structure of the Pfu model is based on the structure of the Taq-FtsY•FfhNG. For Pfu-FtsY, the N and G domain have been colored red and green respectively except for the αN1 and α7 terminal helices highlighted in red and pink. The stretch of basic aminoacids present at the N terminus of αN1 (yellow) clashes with α7. For the N domain, the DX4ELEX2LX3D motifs (Glu47-Asp61 (Pfu) on Glu29-Asp43 (Taq)) were aligned. The entire G domains (Val125-Phe307 (Pfu) on Val104-F292 (Taq)) with the omission of the C-terminal α7 helix were aligned. A similar alignment was made for the Pfu-SRP54 NG (light blue) including Leu39-Asn45 (Pfu) on Leu38-Asn44 (Taq) for the N domain, and Val106-Phe284 (Pfu) on Val104-Phe282 (Taq) for the G domain. The Pfu-SRP54 structure (pdb code 3DM5) used for modeling is reported in a previous article (in press in PloS One). The N-G linkers were omitted. (B) Detail showing the rearrangement undergone by the αN1 and α7 terminal helices at the N/G interface upon complexation.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2572998&req=5

pone-0003619-g006: Model of domain rearrangement in Pfu-FtsY upon its interaction with SRP54.(A) The overall structure of the Pfu model is based on the structure of the Taq-FtsY•FfhNG. For Pfu-FtsY, the N and G domain have been colored red and green respectively except for the αN1 and α7 terminal helices highlighted in red and pink. The stretch of basic aminoacids present at the N terminus of αN1 (yellow) clashes with α7. For the N domain, the DX4ELEX2LX3D motifs (Glu47-Asp61 (Pfu) on Glu29-Asp43 (Taq)) were aligned. The entire G domains (Val125-Phe307 (Pfu) on Val104-F292 (Taq)) with the omission of the C-terminal α7 helix were aligned. A similar alignment was made for the Pfu-SRP54 NG (light blue) including Leu39-Asn45 (Pfu) on Leu38-Asn44 (Taq) for the N domain, and Val106-Phe284 (Pfu) on Val104-Phe282 (Taq) for the G domain. The Pfu-SRP54 structure (pdb code 3DM5) used for modeling is reported in a previous article (in press in PloS One). The N-G linkers were omitted. (B) Detail showing the rearrangement undergone by the αN1 and α7 terminal helices at the N/G interface upon complexation.

Mentions: In the FtsY•SRP54 complex the interface involves both N and G domains: In particular, the N domain ELEX2LX3D motifs present in both SRP54 and FtsY (see the sequence alignment in Figure 1A) come in close contact upon complex formation. A model of the Pfu-FtsY•SRP54 complex was assembled based on our structure of the Taq complex. The N and G domain were aligned independently to generate an NG conformation similar to the one observed in the Taq complex (Figure 6A). In the case of Pfu-FtsY, the N domain has to undergo a rotation and translation to adopt the complexed conformation (Figure 6B). This rotation causes the terminal helices αN1 and α7 to clash, highlighting the requirement for a substantial displacement of αN1. The extent of such steric hindrance is likely to be more important than our model suggests, since the Taq complex structures have shown that α7 repacks more tightly against the NG core interface upon complex formation. The area of overlap maps to the stretch of solvent-exposed basic aminoacids in αN. A recent structure of GDP-bound Taq-FtsY with its αN1 helix deleted revealed that this truncated version of the receptor adopts a conformation close to the one observed in the Taq complex [15].


Structures of the signal recognition particle receptor from the archaeon Pyrococcus furiosus: implications for the targeting step at the membrane.

Egea PF, Tsuruta H, de Leon GP, Napetschnig J, Walter P, Stroud RM - PLoS ONE (2008)

Model of domain rearrangement in Pfu-FtsY upon its interaction with SRP54.(A) The overall structure of the Pfu model is based on the structure of the Taq-FtsY•FfhNG. For Pfu-FtsY, the N and G domain have been colored red and green respectively except for the αN1 and α7 terminal helices highlighted in red and pink. The stretch of basic aminoacids present at the N terminus of αN1 (yellow) clashes with α7. For the N domain, the DX4ELEX2LX3D motifs (Glu47-Asp61 (Pfu) on Glu29-Asp43 (Taq)) were aligned. The entire G domains (Val125-Phe307 (Pfu) on Val104-F292 (Taq)) with the omission of the C-terminal α7 helix were aligned. A similar alignment was made for the Pfu-SRP54 NG (light blue) including Leu39-Asn45 (Pfu) on Leu38-Asn44 (Taq) for the N domain, and Val106-Phe284 (Pfu) on Val104-Phe282 (Taq) for the G domain. The Pfu-SRP54 structure (pdb code 3DM5) used for modeling is reported in a previous article (in press in PloS One). The N-G linkers were omitted. (B) Detail showing the rearrangement undergone by the αN1 and α7 terminal helices at the N/G interface upon complexation.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2572998&req=5

pone-0003619-g006: Model of domain rearrangement in Pfu-FtsY upon its interaction with SRP54.(A) The overall structure of the Pfu model is based on the structure of the Taq-FtsY•FfhNG. For Pfu-FtsY, the N and G domain have been colored red and green respectively except for the αN1 and α7 terminal helices highlighted in red and pink. The stretch of basic aminoacids present at the N terminus of αN1 (yellow) clashes with α7. For the N domain, the DX4ELEX2LX3D motifs (Glu47-Asp61 (Pfu) on Glu29-Asp43 (Taq)) were aligned. The entire G domains (Val125-Phe307 (Pfu) on Val104-F292 (Taq)) with the omission of the C-terminal α7 helix were aligned. A similar alignment was made for the Pfu-SRP54 NG (light blue) including Leu39-Asn45 (Pfu) on Leu38-Asn44 (Taq) for the N domain, and Val106-Phe284 (Pfu) on Val104-Phe282 (Taq) for the G domain. The Pfu-SRP54 structure (pdb code 3DM5) used for modeling is reported in a previous article (in press in PloS One). The N-G linkers were omitted. (B) Detail showing the rearrangement undergone by the αN1 and α7 terminal helices at the N/G interface upon complexation.
Mentions: In the FtsY•SRP54 complex the interface involves both N and G domains: In particular, the N domain ELEX2LX3D motifs present in both SRP54 and FtsY (see the sequence alignment in Figure 1A) come in close contact upon complex formation. A model of the Pfu-FtsY•SRP54 complex was assembled based on our structure of the Taq complex. The N and G domain were aligned independently to generate an NG conformation similar to the one observed in the Taq complex (Figure 6A). In the case of Pfu-FtsY, the N domain has to undergo a rotation and translation to adopt the complexed conformation (Figure 6B). This rotation causes the terminal helices αN1 and α7 to clash, highlighting the requirement for a substantial displacement of αN1. The extent of such steric hindrance is likely to be more important than our model suggests, since the Taq complex structures have shown that α7 repacks more tightly against the NG core interface upon complex formation. The area of overlap maps to the stretch of solvent-exposed basic aminoacids in αN. A recent structure of GDP-bound Taq-FtsY with its αN1 helix deleted revealed that this truncated version of the receptor adopts a conformation close to the one observed in the Taq complex [15].

Bottom Line: The basic charges on the surface of this helix are likely to regulate interactions at the membrane.Small angle X-ray scattering and analytical ultracentrifugation indicate that the crystal structure of Pfu-FtsY correlates well with the average conformation in solution.Based on previous structures of two sub-complexes, we propose a model of the core of archeal and eukaryotic SRP*SR targeting complexes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA. pascal@msg.ucsf.edu

ABSTRACT
In all organisms, a ribonucleoprotein called the signal recognition particle (SRP) and its receptor (SR) target nascent proteins from the ribosome to the translocon for secretion or membrane insertion. We present the first X-ray structures of an archeal FtsY, the receptor from the hyper-thermophile Pyrococcus furiosus (Pfu), in its free and GDP*magnesium-bound forms. The highly charged N-terminal domain of Pfu-FtsY is distinguished by a long N-terminal helix. The basic charges on the surface of this helix are likely to regulate interactions at the membrane. A peripheral GDP bound near a regulatory motif could indicate a site of interaction between the receptor and ribosomal or SRP RNAs. Small angle X-ray scattering and analytical ultracentrifugation indicate that the crystal structure of Pfu-FtsY correlates well with the average conformation in solution. Based on previous structures of two sub-complexes, we propose a model of the core of archeal and eukaryotic SRP*SR targeting complexes.

Show MeSH
Related in: MedlinePlus