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
A model for the association between the SRP and it receptor SR in the targeting complex.(A) Schematic showing the overall organization of the Pfu targeting complex. The core of the SRP RNA is shown with helices 6 and 8, the respective binding sites for the proteins SRP19 and SRP54. In SRP54 the M domain, responsible for both SRP RNA and signal sequence recognition, is connected to the NG domain (GTPase) through a flexible linker (red). Although the NG of SRP54 domain has also been shown to interact loosely with the core of the SRP RNA, for the sake of clarity this is not represented on this schematic. (B) The Pfu protein structures were used to generate this model based on the Taq-FtsY•FfhNG and Mja-SRP complexes structures. FtsY, SRP54 and SRP19 are colored in green, blue and orange respectively. The core of the Mja-SRP RNA, composed of helices 5,6 and 8 is represented in pink. In the SRP54 subunit, the GM linker, colored in red, has been manually repositioned. Nucleotides are represented using space-filling models. At the FtsY•SRP54 interface, the twinned GTP substrates are colored in yellow and the two external nucleosides observed in the Taq-FtsY•FfhNG structure bound to GDP-AlF4 (red asterisk) and in the Pfu-FtsY structure (magenta asterisk) are colored in white. αN1 helices are labeled. The Pfu-SRP19 structure (pdb codes 3DLU and 3DLV) used for modeling has been reported in a previous article (in press in PloS One).
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2572998&req=5

pone-0003619-g007: A model for the association between the SRP and it receptor SR in the targeting complex.(A) Schematic showing the overall organization of the Pfu targeting complex. The core of the SRP RNA is shown with helices 6 and 8, the respective binding sites for the proteins SRP19 and SRP54. In SRP54 the M domain, responsible for both SRP RNA and signal sequence recognition, is connected to the NG domain (GTPase) through a flexible linker (red). Although the NG of SRP54 domain has also been shown to interact loosely with the core of the SRP RNA, for the sake of clarity this is not represented on this schematic. (B) The Pfu protein structures were used to generate this model based on the Taq-FtsY•FfhNG and Mja-SRP complexes structures. FtsY, SRP54 and SRP19 are colored in green, blue and orange respectively. The core of the Mja-SRP RNA, composed of helices 5,6 and 8 is represented in pink. In the SRP54 subunit, the GM linker, colored in red, has been manually repositioned. Nucleotides are represented using space-filling models. At the FtsY•SRP54 interface, the twinned GTP substrates are colored in yellow and the two external nucleosides observed in the Taq-FtsY•FfhNG structure bound to GDP-AlF4 (red asterisk) and in the Pfu-FtsY structure (magenta asterisk) are colored in white. αN1 helices are labeled. The Pfu-SRP19 structure (pdb codes 3DLU and 3DLV) used for modeling has been reported in a previous article (in press in PloS One).

Mentions: The targeting complex is formed when SRP interacts with its receptor (Figure 7A). A functional archeal SRP is organized around two proteins, SRP19 and SRP54 that assemble on SRP RNA. We have also recently reported the structures of the SRP54 and SRP19 from Pfu (in press in PloS One). The present structure of the associated receptor complements this work. Pfu is the first organism where separate structures of all of the proteins present in the targeting complex are available at high resolution. We generated a model of this complex, based on three FtsY•FfhNG heterodimer structures from Taq [6], [7], [27], [28] and the SRP structure from Methanococcus jannaschii (Mja) [29]. In the model, we superposed the Pfu-FtsY (with its two GDPs) and the Pfu-SRP54 NG domain onto the Taq-FtsY•FfhNG structure to generate the equivalent Pfu-FtsY•FfhNG interface (Figure 6A). The NG domain of Mja-SRP was superposed on the FtsY•FfhNG core to model the relative position of the SRP RNA. The Pfu-SRP19 subunit and the Pfu-SRP54 M domain (with the omission of the G-M linker) were then docked, assuming similar, but not necessarily identical relative configurations of the NG and M domains in the SRP and the SRP•SR complexes (Figure 7B and Supplementary Movie S1).


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)

A model for the association between the SRP and it receptor SR in the targeting complex.(A) Schematic showing the overall organization of the Pfu targeting complex. The core of the SRP RNA is shown with helices 6 and 8, the respective binding sites for the proteins SRP19 and SRP54. In SRP54 the M domain, responsible for both SRP RNA and signal sequence recognition, is connected to the NG domain (GTPase) through a flexible linker (red). Although the NG of SRP54 domain has also been shown to interact loosely with the core of the SRP RNA, for the sake of clarity this is not represented on this schematic. (B) The Pfu protein structures were used to generate this model based on the Taq-FtsY•FfhNG and Mja-SRP complexes structures. FtsY, SRP54 and SRP19 are colored in green, blue and orange respectively. The core of the Mja-SRP RNA, composed of helices 5,6 and 8 is represented in pink. In the SRP54 subunit, the GM linker, colored in red, has been manually repositioned. Nucleotides are represented using space-filling models. At the FtsY•SRP54 interface, the twinned GTP substrates are colored in yellow and the two external nucleosides observed in the Taq-FtsY•FfhNG structure bound to GDP-AlF4 (red asterisk) and in the Pfu-FtsY structure (magenta asterisk) are colored in white. αN1 helices are labeled. The Pfu-SRP19 structure (pdb codes 3DLU and 3DLV) used for modeling has been reported in a previous article (in press in PloS One).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0003619-g007: A model for the association between the SRP and it receptor SR in the targeting complex.(A) Schematic showing the overall organization of the Pfu targeting complex. The core of the SRP RNA is shown with helices 6 and 8, the respective binding sites for the proteins SRP19 and SRP54. In SRP54 the M domain, responsible for both SRP RNA and signal sequence recognition, is connected to the NG domain (GTPase) through a flexible linker (red). Although the NG of SRP54 domain has also been shown to interact loosely with the core of the SRP RNA, for the sake of clarity this is not represented on this schematic. (B) The Pfu protein structures were used to generate this model based on the Taq-FtsY•FfhNG and Mja-SRP complexes structures. FtsY, SRP54 and SRP19 are colored in green, blue and orange respectively. The core of the Mja-SRP RNA, composed of helices 5,6 and 8 is represented in pink. In the SRP54 subunit, the GM linker, colored in red, has been manually repositioned. Nucleotides are represented using space-filling models. At the FtsY•SRP54 interface, the twinned GTP substrates are colored in yellow and the two external nucleosides observed in the Taq-FtsY•FfhNG structure bound to GDP-AlF4 (red asterisk) and in the Pfu-FtsY structure (magenta asterisk) are colored in white. αN1 helices are labeled. The Pfu-SRP19 structure (pdb codes 3DLU and 3DLV) used for modeling has been reported in a previous article (in press in PloS One).
Mentions: The targeting complex is formed when SRP interacts with its receptor (Figure 7A). A functional archeal SRP is organized around two proteins, SRP19 and SRP54 that assemble on SRP RNA. We have also recently reported the structures of the SRP54 and SRP19 from Pfu (in press in PloS One). The present structure of the associated receptor complements this work. Pfu is the first organism where separate structures of all of the proteins present in the targeting complex are available at high resolution. We generated a model of this complex, based on three FtsY•FfhNG heterodimer structures from Taq [6], [7], [27], [28] and the SRP structure from Methanococcus jannaschii (Mja) [29]. In the model, we superposed the Pfu-FtsY (with its two GDPs) and the Pfu-SRP54 NG domain onto the Taq-FtsY•FfhNG structure to generate the equivalent Pfu-FtsY•FfhNG interface (Figure 6A). The NG domain of Mja-SRP was superposed on the FtsY•FfhNG core to model the relative position of the SRP RNA. The Pfu-SRP19 subunit and the Pfu-SRP54 M domain (with the omission of the G-M linker) were then docked, assuming similar, but not necessarily identical relative configurations of the NG and M domains in the SRP and the SRP•SR complexes (Figure 7B and Supplementary Movie S1).

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