Crystallographic structure of the amino terminal domain of yeast initiation factor 4A, a representative DEAD-box RNA helicase

RNA

Volumn 5, Issue 12, 1999, Pages 1526-1534

  Johnson, Eric R ^a   Mckay, David B ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Crystal structure; DEAD box; elF4A; RNA helicase

Indexed keywords

INITIATION FACTOR; RNA HELICASE;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; ENZYME STRUCTURE; GENETIC CONSERVATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DEAD-BOX RNA HELICASES; EUKARYOTIC INITIATION FACTOR-4A; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PEPTIDE INITIATION FACTORS; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS; RNA HELICASES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 0032763657     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838299991410     Document Type: Article

References (36)

1. Abrahams JP, Leslie GW. 1996. Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Crystallogr D52:30-42.
2. Bailey S. 1994. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr D50:760-763.
3. Benz J, Trachsel H, Baumann U. 1999. Crystal structure of the ATPase domain of translation initiation factor 4A from Saccharomyces cerevisiae - the prototype of the DEAD box protein family. Structure 7:671-679.
4. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang J-S, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL 1998. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D54:905-921.
5. Cho HS, Ha NC, Kang LW, Chung KM, Back SH, Jang SK, Oh BH. 1998. Crystal structure of RNA helicase from genotype 1b hepatitis C virus. A feasible mechanism of unwinding duplex RNA. J Biol Chem 273:15045-15052.
6. de La Fortelle E, Bricogne G. 1997. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength diffraction methods. Methods Enzymol 276:472-494.
7. Esnouf RM. 1997. An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J Mol Graph Model 15:132-134.
8. Esnouf RM. 1999. Further additions to MolScript version 1.4, including reading and contouring of electron-density maps. Acta Crystallogr D55:938-940.
9. Gorbalenya AE, Koonin EV. 1993. Helicases: Amino acid sequence comparisons and structure-function relationships. Curr Opin Struct Biol 3:419-429.
10. Jaramillo M, Dever TE, Merrick WC, Sonenberg N. 1991. RNA unwinding in translation: Assembly of helicase complex intermediates comprising eukaryotic initiation factors elF-4F and elF-4B. Mol Cell Biol 11:5992-5997.
11. Jones TA, Zhou JY, Cowan SW, Kjeldgaard M. 1991. Improved methods for the building of protein models in electron density maps and the location of errors in these models. Acta Crystallogr A47:110-119.
12. Kim JL, Morgenstern KA, Griffith JP, Dwyer MD, Thomson JA, Murcko MA, Lin C, Caron PR. 1998. Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: The crystal structure provides insights into the mode of unwinding. Structure 6:89-100.
13. Korolev S, Hsieh J, Gauss GH, Lohman TM, Waksman G. 1997. Major domain swiveling revealed by the crystal structures of complexes of E. coli Rep helicase bound to single-stranded DNA and ADP. Cell 90:635-647.
14. Korolev S, Yao N, Lohman TM, Weber PC, Waksman G. 1998. Comparisons between the structures of HCV and Rep helicases reveal structural similarities between SF1 and SF2 super-families of helicases. Protein Sci 7:605-610.
15. Kraulis P. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Appl Cryst 24:946-950.
16. Lorsch JR, Herschlag D. 1998. The DEAD box protein elF4A. 2. A cycle of nucleotide and RNA-dependent conformational changes. Biochemistry 37:2194-2206.
17. Luzzati PV. 1952. Traitment statistique des erreurs dans la determination des structures cristallines. Acta Crystallogr 5:802-810.
18. Methot N, Pause A, Hershey JW, Sonenberg N. 1994. The translation initiation factor elF-4B contains an RNA-binding region that is distinct and independent from its ribonucleoprotein consensus sequence. Mol Cell Biol 14:2307-2316.
19. Otwinowski Z, Minor W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307-326.
20. Pain VM. 1996. Initiation of protein synthesis in eukaryotic cells. Eur J Biochem 236:747-771.
21. Pause A, Sonenberg N. 1992. Mutational analysis of a DEAD box RNA helicase: The mammalian translation initiation factor elF-4A. EMBO J 11:2643-2654.
22. Plumpton M, McGarvey M, Beggs JD. 1994. A dominant negative mutation in the conserved RNA helicase motif "SAT" causes splicing factor PRP2 to stall in spliceosomes. EMBO J 13:879-887.
23. Py B, Higgins CF, Krisch HM, Carpousis AJ. 1996. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature 381: 169-172.
24. Ramakrishnan V, Biou V. 1997. Treatment of multiwavelength anomalous diffraction data as a special case of multiple isomorphous replacement. Methods Enzymol 276:538-557.
25. Rogers GW Jr, Richter NJ, Merrick WC. 1999. Biochemical and kinetic characterization of the RNA helicase activity of eukaryotic initiation factor 4A. J Biol Chem 274:12236-12244.
26. Rozen F, Pelletier J, Trachsel H, Sonenberg N. 1989. A lysine substitution in the ATP-binding site of eucaryotic initiation factor 4A abrogates nucleotide-binding activity. Mol Cell Biol 9:4061-4063.
27. Sayle RA, Milner-White EJ. 1995. RASMOL: Biomolecular graphics for all. Trends Biochem Sci 20:374.
28. Schmid SR, Linder P. 1991. Translation initiation factor 4A from Saccharomyces cerevisiae: Analysis of residues conserved in the D-E-A-D family of RNA helicases. Mol Cell Biol 11:3463-3471.
29. Smith CA, Rayment I. 1996. Active site comparisons highlight structural similarities between myosin and other P-loop proteins. Biophys J 70:1590-1602.
30. Staley JP, Guthrie C. 1998. Mechanical devices of the spliceosome: Motors, clocks, springs, and things. Cell 92:315-326.
31. Story RM, Steitz TA. 1992. Structure of the recA protein-ADP complex. Nature 355:374-376.
32. Subramanya HS, Bird LE, Brannigan JA, Wigley DB. 1996. Crystal structure of a DExx box DNA helicase. Nature 384:379-383.
33. Terwilliger TC, Berendzen J. 1999. Automated structure solution for MIR and MAD. Acta Crystallogr D55:849-861.
34. Velankar SS, Soultanas P, Dillingham MS, Subramanya HS, Wigley DB. 1999. Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell 97:75-84.
35. Venema J, Tollervey D. 1995. Processing of pre-ribosomal RNA in Saccharomyces cerevisiae. Yeast 11:1629-1650.
36. Yao N, Hesson T, Cable M, Hong Z, Kwong AD, Le HV, Weber PC. 1997. Structure of the hepatitis C virus RNA helicase domain. Nat Struct Biol 4:463-467.