Structure of a GDP:AlF4 Complex of the SRP GTPases Ffh and FtsY, and Identification of a Peripheral Nucleotide Interaction Site

Overview

Journal J Mol Biol

Publisher Elsevier

Specialties Microbiology
Molecular Biology

Date 2006 Jun 20

PMID 16780874

Citations 18

Authors

Pamela J Focia

Joseph Gawronski-Salerno

John S Coon 5th

Douglas M Freymann

Affiliations

Soon will be listed here.

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.

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References

Schindelin H, Kisker C, Schlessman J, Howard J, Rees D . Structure of ADP x AIF4(-)-stabilized nitrogenase complex and its implications for signal transduction. Nature. 1997; 387(6631):370-6. DOI: 10.1038/387370a0. View

Aittaleb M, Rashid R, Chen Q, Palmer J, Daniels C, Li H . Structure and function of archaeal box C/D sRNP core proteins. Nat Struct Biol. 2003; 10(4):256-63. DOI: 10.1038/nsb905. View

Freymann D, Keenan R, Stroud R, Walter P . Structure of the conserved GTPase domain of the signal recognition particle. Nature. 1997; 385(6614):361-4. DOI: 10.1038/385361a0. View

Perrakis A, Sixma T, Wilson K, Lamzin V . wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models. Acta Crystallogr D Biol Crystallogr. 1997; 53(Pt 4):448-55. DOI: 10.1107/S0907444997005696. View

Schmitz U, James T, Lukavsky P, Walter P . Structure of the most conserved internal loop in SRP RNA. Nat Struct Biol. 1999; 6(7):634-8. DOI: 10.1038/10683. View

Ollis D, Brick P, Hamlin R, Xuong N, Steitz T . Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. Nature. 1985; 313(6005):762-6. DOI: 10.1038/313762a0. View

Kleywegt G, Jones T . Detecting folding motifs and similarities in protein structures. Methods Enzymol. 1997; 277:525-45. DOI: 10.1016/s0076-6879(97)77029-0. View

Rould M, Perona J, Steitz T . Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase. Nature. 1991; 352(6332):213-8. DOI: 10.1038/352213a0. View

Silva M, de Paula Silva C, Iulek J, Thiemann O . Three-dimensional structure of human adenine phosphoribosyltransferase and its relation to DHA-urolithiasis. Biochemistry. 2004; 43(24):7663-71. DOI: 10.1021/bi0360758. View

10.

Thomas C, Du X, Li P, Wang Y, Ross E, Sprang S . Uncoupling conformational change from GTP hydrolysis in a heterotrimeric G protein alpha-subunit. Proc Natl Acad Sci U S A. 2004; 101(20):7560-5. PMC: 419645. DOI: 10.1073/pnas.0304091101. View

11.

Batey R, Rambo R, Lucast L, Rha B, Doudna J . Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science. 2000; 287(5456):1232-9. DOI: 10.1126/science.287.5456.1232. View

12.

Bernstein H, Poritz M, Strub K, Hoben P, Brenner S, Walter P . Model for signal sequence recognition from amino-acid sequence of 54K subunit of signal recognition particle. Nature. 1989; 340(6233):482-6. DOI: 10.1038/340482a0. View

13.

Buskiewicz I, Peske F, Wieden H, Gryczynski I, Rodnina M, Wintermeyer W . Conformations of the signal recognition particle protein Ffh from Escherichia coli as determined by FRET. J Mol Biol. 2005; 351(2):417-30. DOI: 10.1016/j.jmb.2005.06.023. View

14.

Vetter I, Wittinghofer A . The guanine nucleotide-binding switch in three dimensions. Science. 2001; 294(5545):1299-304. DOI: 10.1126/science.1062023. View

15.

Egea P, Shan S, Napetschnig J, Savage D, Walter P, Stroud R . Substrate twinning activates the signal recognition particle and its receptor. Nature. 2004; 427(6971):215-21. DOI: 10.1038/nature02250. View

16.

Schlichting I, Reinstein J . pH influences fluoride coordination number of the AlFx phosphoryl transfer transition state analog. Nat Struct Biol. 1999; 6(8):721-3. DOI: 10.1038/11485. View

17.

Powers T, Walter P . Reciprocal stimulation of GTP hydrolysis by two directly interacting GTPases. Science. 1995; 269(5229):1422-4. DOI: 10.1126/science.7660124. View

18.

Peluso P, Shan S, Nock S, Herschlag D, Walter P . Role of SRP RNA in the GTPase cycles of Ffh and FtsY. Biochemistry. 2001; 40(50):15224-33. DOI: 10.1021/bi011639y. View

19.

Aldaz H, Rice L, Stearns T, Agard D . Insights into microtubule nucleation from the crystal structure of human gamma-tubulin. Nature. 2005; 435(7041):523-7. DOI: 10.1038/nature03586. View

20.

Rittinger K, Walker P, Eccleston J, Smerdon S, Gamblin S . Structure at 1.65 A of RhoA and its GTPase-activating protein in complex with a transition-state analogue. Nature. 1997; 389(6652):758-62. DOI: 10.1038/39651. View