PDBsum entry 2cnw

Signal recognition

PDB id: 2cnw

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

Protein chains

O07347  (SRP54_THEAQ) -  Signal recognition particle protein from Thermus aquaticus

Seq: 430 a.a.

Struc: 290 a.a.

Protein chains

P83749  (FTSY_THEAQ) -  Signal recognition particle receptor FtsY from Thermus aquaticus

Seq: 304 a.a.

Struc: 281 a.a.

Protein chain

P83749  (FTSY_THEAQ) -  Signal recognition particle receptor FtsY from Thermus aquaticus

Seq: 304 a.a.

Struc: 260 a.a.

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.