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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.

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The N domain.(A) Stabilization of the highly charged N domain of apo Pfu-FtsY through an intricate network of salt bridges and hydrogen bonds. 2.2Å resolution likelihood-weighted 2mFo-DFc Fourier difference electron density map contoured at 1.4σ showing the most solvent-exposed tip of the N domain. A subset of basic and acidic side-chains is shown. (B) Properties of the N-terminal helix αN1 of the N domain. The helix αN1 packs tightly against the G domain helices α6 and α7 (C-terminal helix). Conserved hydrophobic residues contributing to the interaction between the N-terminus of the N domain and the C-terminus of the G domain at the N/G interface are labeled. Solvent exposed basic residues are also indicated. Helices are labeled. These properties appear to be conserved in all archeal receptor sequences.
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pone-0003619-g003: The N domain.(A) Stabilization of the highly charged N domain of apo Pfu-FtsY through an intricate network of salt bridges and hydrogen bonds. 2.2Å resolution likelihood-weighted 2mFo-DFc Fourier difference electron density map contoured at 1.4σ showing the most solvent-exposed tip of the N domain. A subset of basic and acidic side-chains is shown. (B) Properties of the N-terminal helix αN1 of the N domain. The helix αN1 packs tightly against the G domain helices α6 and α7 (C-terminal helix). Conserved hydrophobic residues contributing to the interaction between the N-terminus of the N domain and the C-terminus of the G domain at the N/G interface are labeled. Solvent exposed basic residues are also indicated. Helices are labeled. These properties appear to be conserved in all archeal receptor sequences.

Mentions: The N domain of Pfu-FtsY is very rich in charged residues (30 acidic and 25 basic residues out of a total of 110 residues representing 50%). These residues contribute to the high thermo-stability of Pfu-FtsY through an intricate network of intra-molecular salt bridges and hydrogen bonds that stabilize the overall fold of the N domain (Figure 3A). At the C terminal end of helix αN1 the carboxylate groups from residues Glu21 and Glu24 interact with the amino group of Lys89 of helix αN3. In a similar fashion, Glu23 on helix αN1 interacts with Lys44 from helix αN2. Such extended ion-pair networks contribute to thermostability in proteins [17]. The N-terminus of helix αN1 is characterized by solvent exposed basic residues (Figure 3B) and packs tightly against the G domain; in particular with helices α6 and the C-terminal helix α7. Sequence analysis suggests that these features are conserved throughout all archeal receptors (Supplementary Figure S2). These clusters of solvent-exposed basic residues on one face of αN1 and the surface of the N domain seem to be in an ideal position for either membrane anchoring, for example, through lysine or arginine “snorkeling” to negatively charged phospholipidic head groups, or for interaction with the ribosomal and/or the SRP RNAs.


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)

The N domain.(A) Stabilization of the highly charged N domain of apo Pfu-FtsY through an intricate network of salt bridges and hydrogen bonds. 2.2Å resolution likelihood-weighted 2mFo-DFc Fourier difference electron density map contoured at 1.4σ showing the most solvent-exposed tip of the N domain. A subset of basic and acidic side-chains is shown. (B) Properties of the N-terminal helix αN1 of the N domain. The helix αN1 packs tightly against the G domain helices α6 and α7 (C-terminal helix). Conserved hydrophobic residues contributing to the interaction between the N-terminus of the N domain and the C-terminus of the G domain at the N/G interface are labeled. Solvent exposed basic residues are also indicated. Helices are labeled. These properties appear to be conserved in all archeal receptor sequences.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0003619-g003: The N domain.(A) Stabilization of the highly charged N domain of apo Pfu-FtsY through an intricate network of salt bridges and hydrogen bonds. 2.2Å resolution likelihood-weighted 2mFo-DFc Fourier difference electron density map contoured at 1.4σ showing the most solvent-exposed tip of the N domain. A subset of basic and acidic side-chains is shown. (B) Properties of the N-terminal helix αN1 of the N domain. The helix αN1 packs tightly against the G domain helices α6 and α7 (C-terminal helix). Conserved hydrophobic residues contributing to the interaction between the N-terminus of the N domain and the C-terminus of the G domain at the N/G interface are labeled. Solvent exposed basic residues are also indicated. Helices are labeled. These properties appear to be conserved in all archeal receptor sequences.
Mentions: The N domain of Pfu-FtsY is very rich in charged residues (30 acidic and 25 basic residues out of a total of 110 residues representing 50%). These residues contribute to the high thermo-stability of Pfu-FtsY through an intricate network of intra-molecular salt bridges and hydrogen bonds that stabilize the overall fold of the N domain (Figure 3A). At the C terminal end of helix αN1 the carboxylate groups from residues Glu21 and Glu24 interact with the amino group of Lys89 of helix αN3. In a similar fashion, Glu23 on helix αN1 interacts with Lys44 from helix αN2. Such extended ion-pair networks contribute to thermostability in proteins [17]. The N-terminus of helix αN1 is characterized by solvent exposed basic residues (Figure 3B) and packs tightly against the G domain; in particular with helices α6 and the C-terminal helix α7. Sequence analysis suggests that these features are conserved throughout all archeal receptors (Supplementary Figure S2). These clusters of solvent-exposed basic residues on one face of αN1 and the surface of the N domain seem to be in an ideal position for either membrane anchoring, for example, through lysine or arginine “snorkeling” to negatively charged phospholipidic head groups, or for interaction with the ribosomal and/or the SRP RNAs.

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