Initiation Factor 2 Crystal Structure Reveals a Different Domain Organization from Eukaryotic Initiation Factor 5B and Mechanism Among Translational GTPases

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2013 Sep 14

PMID 24029018

Citations 18

Authors

Daniel Eiler

Jinzhong Lin

Angelita Simonetti

Bruno P Klaholz

Thomas A Steitz

Affiliations

Soon will be listed here.

Abstract

The initiation of protein synthesis uses initiation factor 2 (IF2) in prokaryotes and a related protein named eukaryotic initiation factor 5B (eIF5B) in eukaryotes. IF2 is a GTPase that positions the initiator tRNA on the 30S ribosomal initiation complex and stimulates its assembly to the 50S ribosomal subunit to make the 70S ribosome. The 3.1-Å resolution X-ray crystal structures of the full-length Thermus thermophilus apo IF2 and its complex with GDP presented here exhibit two different conformations (all of its domains except C2 domain are visible). Unlike all other translational GTPases, IF2 does not have an effecter domain that stably contacts the switch II region of the GTPase domain. The domain organization of IF2 is inconsistent with the "articulated lever" mechanism of communication between the GTPase and initiator tRNA binding domains that has been proposed for eIF5B. Previous cryo-electron microscopy reconstructions, NMR experiments, and this structure show that IF2 transitions from being flexible in solution to an extended conformation when interacting with ribosomal complexes.

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References

Roll-Mecak A, Cao C, Dever T, Burley S . X-Ray structures of the universal translation initiation factor IF2/eIF5B: conformational changes on GDP and GTP binding. Cell. 2000; 103(5):781-92. DOI: 10.1016/s0092-8674(00)00181-1. View

Myasnikov A, Marzi S, Simonetti A, Giuliodori A, Gualerzi C, Yusupova G . Conformational transition of initiation factor 2 from the GTP- to GDP-bound state visualized on the ribosome. Nat Struct Mol Biol. 2005; 12(12):1145-9. DOI: 10.1038/nsmb1012. View

Antoun A, Pavlov M, Tenson T, Ehrenberg M M . Ribosome formation from subunits studied by stopped-flow and Rayleigh light scattering. Biol Proced Online. 2004; 6:35-54. PMC: 389903. DOI: 10.1251/bpo71. View

Milon P, Carotti M, Konevega A, Wintermeyer W, Rodnina M, Gualerzi C . The ribosome-bound initiation factor 2 recruits initiator tRNA to the 30S initiation complex. EMBO Rep. 2010; 11(4):312-6. PMC: 2854590. DOI: 10.1038/embor.2010.12. View

Bourne H, Sanders D, McCormick F . The GTPase superfamily: conserved structure and molecular mechanism. Nature. 1991; 349(6305):117-27. DOI: 10.1038/349117a0. View

Moreno J, Drskjotersen L, Kristensen J, Mortensen K . Characterization of the domains of E. coli initiation factor IF2 responsible for recognition of the ribosome. FEBS Lett. 1999; 455(1-2):130-4. DOI: 10.1016/s0014-5793(99)00858-3. View

Wienk H, Tomaselli S, Bernard C, Spurio R, Picone D, Gualerzi C . Solution structure of the C1-subdomain of Bacillus stearothermophilus translation initiation factor IF2. Protein Sci. 2005; 14(9):2461-8. PMC: 2253463. DOI: 10.1110/ps.051531305. View

Adams P, Afonine P, Bunkoczi G, Chen V, Davis I, Echols N . PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr. 2010; 66(Pt 2):213-21. PMC: 2815670. DOI: 10.1107/S0907444909052925. View

Hauryliuk V, Hansson S, Ehrenberg M . Cofactor dependent conformational switching of GTPases. Biophys J. 2008; 95(4):1704-15. PMC: 2483772. DOI: 10.1529/biophysj.107.127290. View

10.

Julian P, Milon P, Agirrezabala X, Lasso G, Gil D, Rodnina M . The Cryo-EM structure of a complete 30S translation initiation complex from Escherichia coli. PLoS Biol. 2011; 9(7):e1001095. PMC: 3130014. DOI: 10.1371/journal.pbio.1001095. View

11.

Milon P, Tischenko E, Tomsic J, Caserta E, Folkers G, La Teana A . The nucleotide-binding site of bacterial translation initiation factor 2 (IF2) as a metabolic sensor. Proc Natl Acad Sci U S A. 2006; 103(38):13962-7. PMC: 1599896. DOI: 10.1073/pnas.0606384103. View

12.

Winn M, Ballard C, Cowtan K, Dodson E, Emsley P, Evans P . Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr. 2011; 67(Pt 4):235-42. PMC: 3069738. DOI: 10.1107/S0907444910045749. View

13.

Petersen H, Roll T, GRUNBERG-MANAGO M, Clark B . Specific interaction of initiation factor IF2 of E. coli with formylmethionyl-tRNA f Met. Biochem Biophys Res Commun. 1979; 91(3):1068-74. DOI: 10.1016/0006-291x(79)91989-2. View

14.

Caserta E, Ferrara C, Milon P, Fabbretti A, Rocchetti A, Tomsic J . Ribosomal interaction of Bacillus stearothermophilus translation initiation factor IF2: characterization of the active sites. J Mol Biol. 2009; 396(1):118-29. DOI: 10.1016/j.jmb.2009.11.026. View

15.

Otwinowski Z, Minor W . Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997; 276:307-26. DOI: 10.1016/S0076-6879(97)76066-X. View

16.

La Teana A, Pon C, Gualerzi C . Late events in translation initiation. Adjustment of fMet-tRNA in the ribosomal P-site. J Mol Biol. 1996; 256(4):667-75. DOI: 10.1006/jmbi.1996.0116. View

17.

Roll-Mecak A, Shin B, Dever T, Burley S . Engaging the ribosome: universal IFs of translation. Trends Biochem Sci. 2001; 26(12):705-9. DOI: 10.1016/s0968-0004(01)02024-2. View

18.

Simonetti A, Marzi S, Fabbretti A, Hazemann I, Jenner L, Urzhumtsev A . Structure of the protein core of translation initiation factor 2 in apo, GTP-bound and GDP-bound forms. Acta Crystallogr D Biol Crystallogr. 2013; 69(Pt 6):925-33. PMC: 3663118. DOI: 10.1107/S0907444913006422. View

19.

Kapralou S, Fabbretti A, Garulli C, Spurio R, Gualerzi C, Dahlberg A . Translation initiation factor IF1 of Bacillus stearothermophilus and Thermus thermophilus substitute for Escherichia coli IF1 in vivo and in vitro without a direct IF1-IF2 interaction. Mol Microbiol. 2008; 70(6):1368-77. PMC: 2614455. DOI: 10.1111/j.1365-2958.2008.06466.x. View

20.

Marshall R, Dorywalska M, Puglisi J . Irreversible chemical steps control intersubunit dynamics during translation. Proc Natl Acad Sci U S A. 2008; 105(40):15364-9. PMC: 2563075. DOI: 10.1073/pnas.0805299105. View