Crystal Structure and RNA Binding of the Tex Protein from Pseudomonas aeruginosa

Journal of Molecular Biology

Volumn 377, Issue 5, 2008, Pages 1460-1473

  Johnson, Sean J ^a   Close, Devin ^b   Robinson, Howard ^c   Vallet Gely, Isabelle ^d   Dove, Simon L ^d   Hill, Christopher P ^b  

^a UTAH STATE UNIVERSITY   (United States)

^b UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^c BROOKHAVEN NATIONAL LABORATORY   (United States)

^d HARVARD MEDICAL SCHOOL   (United States)

Author keywords

S1 domain; Spt6; Tex; transcription; x ray crystallography

Indexed keywords

BACTERIAL PROTEIN; NUCLEASE; PROTEIN TEX; RNA POLYMERASE; SINGLE STRANDED RNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR SPT6; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN STRUCTURE; PSEUDOMONAS AERUGINOSA; RNA BINDING; SEQUENCE ALIGNMENT;

BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA; PSEUDOMONAS AERUGINOSA;

EID: 40849094161     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.01.096     Document Type: Article

References (53)

1. Fuchs T.M., Deppisch H., Scarlato V., and Gross R. A new gene locus of Bordetella pertussis defines a novel family of prokaryotic transcriptional accessory proteins. J. Bacteriol. 178 (1996) 4445-4452
2. Aravind L., Makarova K.S., and Koonin E.V. Survey and summary: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res. 28 (2000) 3417-3432
3. He X., Thornton J., Carmicle-Davis S., and McDaniel L.S. Tex, a putative transcriptional accessory factor, is involved in pathogen fitness in Streptococcus pneumoniae. Microb. Pathog. 41 (2006) 199-206
4. Potvin E., Lehoux D.E., Kukavica-Ibrulj I., Richard K.L., Sanschagrin F., Lau G.W., and Levesque R.C. In vivo functional genomics of Pseudomonas aeruginosa for high-throughput screening of new virulence factors and antibacterial targets. Environ. Microbiol. 5 (2003) 1294-1308
5. Anantharaman V., Koonin E.V., and Aravind L. Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res. 30 (2002) 1427-1464
6. Kaplan C.D., Morris J.R., Wu C., and Winston F. Spt5 and spt6 are associated with active transcription and have characteristics of general elongation factors in D. melanogaster. Genes Dev. 14 (2000) 2623-2634
7. Ponting C.P. Novel domains and orthologues of eukaryotic transcription elongation factors. Nucleic Acids Res. 30 (2002) 3643-3652
8. Doolittle R.F. Urfs and Orfs: A Primer on How to Analyze Derived Amino Acid Sequences (1986), University Science Books, Mill Valley, CA
9. Adkins M.W., and Tyler J.K. Transcriptional activators are dispensable for transcription in the absence of Spt6-mediated chromatin reassembly of promoter regions. Mol. Cell 21 (2006) 405-416
10. Bortvin A., and Winston F. Evidence that Spt6p controls chromatin structure by a direct interaction with histones. Science 272 (1996) 1473-1476
11. Kaplan C.D., Laprade L., and Winston F. Transcription elongation factors repress transcription initiation from cryptic sites. Science 301 (2003) 1096-1099
12. Yoh S.M., Cho H., Pickle L., Evans R.M., and Jones K.A. The Spt6 SH2 domain binds Ser2-P RNAPII to direct Iws1-dependent mRNA splicing and export. Genes Dev. 21 (2007) 160-174
13. Andrulis E.D., Werner J., Nazarian A., Erdjument-Bromage H., Tempst P., and Lis J.T. The RNA processing exosome is linked to elongating RNA polymerase II in Drosophila. Nature 420 (2002) 837-841
14. Carpousis A.J. The Escherichia coli RNA degradosome: structure, function and relationship in other ribonucleolytic multienzyme complexes. Biochem. Soc. Trans. 30 (2002) 150-155
15. Davis I.W., Leaver-Fay A., Chen V.B., Block J.N., Kapral G.J., Wang X., et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35 (2007) W375-W383
16. Aravind L., Anantharaman V., Balaji S., Babu M.M., and Iyer L.M. The many faces of the helix-turn-helix domain: transcription regulation and beyond. FEMS Microbiol. Rev. 29 (2005) 231-262
17. Buttner K., Nehring S., and Hopfner K.P. Structural basis for DNA duplex separation by a superfamily-2 helicase. Nat. Struct. Mol. Biol. 14 (2007) 647-652
18. Holm L., and Sander C. Touring protein fold space with Dali/FSSP. Nucleic Acids Res. 26 (1998) 316-319
19. Landau M., Mayrose I., Rosenberg Y., Glaser F., Martz E., Pupko T., and Ben-Tal N. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res. 33 (2005) W299-W302
20. Letunic I., Copley R.R., Pils B., Pinkert S., Schultz J., and Bork P. SMART 5: domains in the context of genomes and networks. Nucleic Acids Res. 34 (2006) D257-D260
21. Rocha E.P., Cornet E., and Michel B. Comparative and evolutionary analysis of the bacterial homologous recombination systems. PLoS Genet. 1 (2005) e15
22. Ichiyanagi K., Iwasaki H., Hishida T., and Shinagawa H. Mutational analysis on structure-function relationship of a holliday junction specific endonuclease RuvC. Genes Cells 3 (1998) 575-586
23. Yoshikawa M., Iwasaki H., and Shinagawa H. Evidence that phenylalanine 69 in Escherichia coli RuvC resolvase forms a stacking interaction during binding and destabilization of a Holliday junction DNA substrate. J. Biol. Chem. 276 (2001) 10432-10436
24. Ariyoshi M., Vassylyev D.G., Iwasaki H., Nakamura H., Shinagawa H., and Morikawa K. Atomic structure of the RuvC resolvase: a holliday junction-specific endonuclease from E. coli. Cell 78 (1994) 1063-1072
25. Saito A., Iwasaki H., Ariyoshi M., Morikawa K., and Shinagawa H. Identification of four acidic amino acids that constitute the catalytic center of the RuvC Holliday junction resolvase. Proc. Natl Acad. Sci. USA 92 (1995) 7470-7474
26. Yoshikawa M., Iwasaki H., Kinoshita K., and Shinagawa H. Two basic residues, Lys-107 and Lys-118, of RuvC resolvase are involved in critical contacts with the Holliday junction for its resolution. Genes Cells 5 (2000) 803-813
27. Shao X., and Grishin N.V. Common fold in helix-hairpin-helix proteins. Nucleic Acids Res. 28 (2000) 2643-2650
28. Bycroft M., Hubbard T.J., Proctor M., Freund S.M., and Murzin A.G. The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold. Cell 88 (1997) 235-242
29. Subramanian A.R. Structure and functions of ribosomal protein S1. Prog. Nucleic Acid Res. Mol. Biol. 28 (1983) 101-142
30. Theobald D.L., Mitton-Fry R.M., and Wuttke D.S. Nucleic acid recognition by OB-fold proteins. Annu. Rev. Biophys. Biomol. Struct. 32 (2003) 115-133
31. Amblar M., Barbas A., Gomez-Puertas P., and Arraiano C.M. The role of the S1 domain in exoribonucleolytic activity: substrate specificity and multimerization. RNA 13 (2007) 317-327
32. Schubert M., Edge R.E., Lario P., Cook M.A., Strynadka N.C., Mackie G.A., and McIntosh L.P. Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces. J. Mol. Biol. 341 (2004) 37-54
33. Hill J.J., and Royer C.A. Fluorescence approaches to study of protein-nucleic acid complexation. Methods Enzymol. 278 (1997) 390-416
34. Stickney L.M., Hankins J.S., Miao X., and Mackie G.A. Function of the conserved S1 and KH domains in polynucleotide phosphorylase. J. Bacteriol. 187 (2005) 7214-7221
35. Callaghan A.J., Marcaida M.J., Stead J.A., McDowall K.J., Scott W.G., and Luisi B.F. Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover. Nature 437 (2005) 1187-1191
36. Yatime L., Schmitt E., Blanquet S., and Mechulam Y. Structure-function relationships of the intact aIF2alpha subunit from the archaeon Pyrococcus abyssi. Biochemistry 44 (2005) 8749-8756
37. Todone F., Brick P., Werner F., Weinzierl R.O., and Onesti S. Structure of an archaeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex. Mol. Cell 8 (2001) 1137-1143
38. Meka H., Werner F., Cordell S.C., Onesti S., and Brick P. Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II. Nucleic Acids Res. 33 (2005) 6435-6444
39. Maclennan A.J., and Shaw G. A yeast SH2 domain. Trends Biochem. Sci. 18 (1993) 464-465
40. Grune T., Brzeski J., Eberharter A., Clapier C.R., Corona D.F., Becker P.B., and Muller C.W. Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. Mol. Cell 12 (2003) 449-460
41. Studier F.W. Protein production by auto-induction in high density shaking cultures. Protein Expr. Purif. 41 (2005) 207-234
42. Van Duyne G.D., Standaert R.F., Karplus P.A., Schreiber S.L., and Clardy J. Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J. Mol. Biol. 229 (1993) 105-124
43. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. In: Carter J.C.W., and Sweet R.M. (Eds). Methods in Enzymology. Macromolecular Crystallography, Part A vol. 276 (1997), Academic Press, New York, NY 307-326
44. Terwilliger T.C., and Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr., Sect. D: Biol. Crystallogr. 55 (1999) 849-861
45. Terwilliger T.C. Maximum-likelihood density modification. Acta Crystallogr., Sect. D: Biol. Crystallogr. 56 (2000) 965-972
46. McCoy A.J., Grosse-Kunstleve R.W., Storoni L.C., and Read R.J. Likelihood-enhanced fast translation functions. Acta Crystallogr., Sect. D: Biol. Crystallogr. 61 (2005) 458-464
47. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr., Sect. D: Biol. Crystallogr. 54 (1998) 905-921
48. Adams P.D., Grosse-Kunstleve R.W., Hung L.W., Ioerger T.R., McCoy A.J., Moriarty N.W., et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr., Sect. D: Biol. Crystallogr. 58 (2002) 1948-1954
49. Collaborative Computational Project. The CCP4 suite: programs for protein crystallography. Acta Crystallogr., Sect. D: Biol. Crystallogr. 50 (1994) 760-763
50. Jones T.A., Zou J.-Y., Cowan S.W., and Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A47 (1991) 110-119
51. Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr., Sect. D: Biol. Crystallogr. 60 (2004) 2126-2132
52. DeLano W.L. The PyMOL Molecular Graphics System (2002), DeLano Scientific, Palo Alto, CA
53. Hoffmann K.M., Williams D., Shafer W.M., and Brennan R.G. Characterization of the multiple transferable resistance repressor, MtrR, from Neisseria gonorrhoeae. J. Bacteriol. 187 (2005) 5008-5012