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Volumn 287, Issue 5456, 2000, Pages 1232-1239

Crystal structure of the ribonucleoprotein core of the signal recognition particle

Author keywords

[No Author keywords available]

Indexed keywords

RNA; SIGNAL RECOGNITION PARTICLE;

EID: 0034681490     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.287.5456.1232     Document Type: Article
Times cited : (319)

References (52)
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    • A fragment of the E. coli Ffh corresponding to residues 298 to 453 was probed with V8 and trypsin proteases in the presence and absence of RNA under conditions that yield limited cleavage of the protein. Samples of the proteolytic reaction were taken between 5 min and 1 hour and subjected to matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry [R. C. Beavis and B. T. Chait, Methods Enzymol. 270, 519 (1996)]. Although the free protein was rapidly proteolyzed (<5 min), binding of RNA protected a region corresponding to residues 318 to 432. Further mapping yielded a minimal M domain comprising residues 328 to 432 that still binds to the 4.5S RNA with the same affinity as that of full-length Ffh. This construct consists of the signal sequence binding region as well as all of the universally conserved amino acids implicated in RNA recognition (Fig. 1D). Cys-406 was mutated to Ser to avoid oxidation that otherwise destroys RNA binding activity (24). In the RNA, the GGAA tetraloop was changed to GAAA to promote RNA-RNA interactions in the crystal lattice.
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    • note
    • d.
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    • The least-squares superposition of backbone a carbons corresponding to the RNA binding region of the bound M domain (E. coli residues 376 to 421), Thermus aquaticus [Protein Data Bank (PDB) accession number 2ffh], and human M domain (1QB2) were performed with LSQMAN [G. J. Kleywegt and T. A. Jones, CCP4 Newslett. 31, 9 (1994)]. The backbone root mean square deviation (rmsd) between the E. coli and T. aquaticus M domains is 0.68 Å, and 0.66 Å between the E. coli and human M domains.
    • (1994) CCP4 Newslett. , vol.31 , pp. 9
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    • Luisi, B.1
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    • 2-ethanol solution and incubation at 90°C for 1 min. The cleavage products were resolved by electrophoresis on a 12% denaturing polyacrylamide gel. The band intensities were quantified by phosphorimaging and the extent of interference determined as described [S. P. Ryder and S. A. Strobel, Methods 18, 38 (1999)].
    • (1999) Methods , vol.18 , pp. 38
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    • 2-ethanol solution and incubation at 90°C for 1 min. The cleavage products were resolved by electrophoresis on a 12% denaturing polyacrylamide gel. The band intensities were quantified by phosphorimaging and the extent of interference determined as described [S. P. Ryder and S. A. Strobel, Methods 18, 38 (1999)].
    • (1999) Methods , vol.18 , pp. 38
    • Ryder, S.P.1    Strobel, S.A.2
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    • note
    • A number of other nucleotide analogs, including 2′ deoxyadenosine, diamino purine, inosine, and N-methyl guanosine, have also been used, and the results are consistent with the crystal structure.
  • 40
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    • The A39U point mutation in the context of the E4 construct was also tested and failed to support growth
    • The A39U point mutation in the context of the E4 construct was also tested and failed to support growth.
  • 52
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    • We thank S. Brown for providing the 4.55 RNA conditionally deficient strains of E. coli and helpful advice; C. Ogata for time and assistance at beamline X4A of the National Synchrotron Light Source, Brookhaven National Laboratory; T. Earnest for support at beamline 5.0.2 of the Advanced Light Source, Lawrence Berkeley National Laboratory; R. Hanna, J. Kieft, A. Luptak, and M. Talavera for help with beam-line data collection and useful discussions; P. Adams and L. Rice for assistance with the refinement; the staff of the Yale Center for Structural Biology for cristallographic and computational support; S. Strobel for providing the nucleotide analogs and for helpful discussions; S. Basu, J. Cate, J. Davis, T. Griffin, J. Ippolito, S. Ryder, P. Scamborova, P. Sigler, and T. Steitz for many helpful discussions; and J. Cate, J. Kieft, V. Rath, and S. Strobel for critically reading the manuscript. We are particularly indebted to A. Ferré-D'Amaré for excellent advice and support throughout this project. This project was funded in part by a postdoctoral fellowship from the Jane Coffin Childs Memorial Fund for Medical Research (R.T.B.), a Howard Hughes Medical Institute (HHMI) summer fellowship (B.R.), and by support from the NIH, HHMI, and the David and Lucile Packard Foundation. J.A.D. is a Fellow of the David and Lucile Packard Foundation and an Assistant Investigator of HHMI. Coordinates of the SRP core and structure factor amplitudes have been deposited in the PDB (accession code 1DUL). Coordinates are also available at www.csb.yale.edu/ people/doudna/doudna_people.html.


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