Crystal structure of the bacteriophage T4 latetranscription coactivator gp33 with the β-subunit flap domain of Escherichia coli RNA polymerase

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 50, 2011, Pages 19961-19966

  Twist, Kelly Anne F ^a,d   Campbell, Elizabeth A ^a   Deighan, Padraig ^b   Nechaev, Sergei ^c,e   Jain, Vikas ^c,f   Geiduschek, E Peter ^c   Hochschild, Ann ^b   Darst, Seth A ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c SECTION OF MOLECULAR BIOLOGY   (United States)

^d MONASH UNIVERSITY   (Australia)

^e NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^f INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH BHOPAL   (India)

Author keywords

Gp33; Replication coupled gene expression; X ray crystallography

Indexed keywords

BACTERIAL PROTEIN; PROTEIN GP33; RNA POLYMERASE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BACTERIOPHAGE T4; COMPLEX FORMATION; CRYSTAL STRUCTURE; CRYSTALLIZATION; ESCHERICHIA COLI; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; TRANSCRIPTION INITIATION;

AMINO ACID SEQUENCE; BACTERIOPHAGE T4; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS, GENETIC; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS; SEQUENCE HOMOLOGY, AMINO ACID; SIGMA FACTOR; TRANS-ACTIVATORS; TRANSCRIPTION, GENETIC; VIRAL PROTEINS;

EID: 84055187722     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1113328108     Document Type: Article

References (42)

1. Murakami K, Masuda S, Campbell EA, Muzzin O, Darst SA (2002) Structural basis of transcription initiation: An RNA polymerase holoenzyme/DNA complex. Science 296:1285-1290. (Pubitemid 34522778)
2. Murakami K, Masuda S, Darst SA (2002) Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution. Science 296:1280-1284. (Pubitemid 34522777)
3. Rhodius VA, Busby SJ (1998) Positive activation of gene expression. Curr Opin Microbiol 1:152-159. (Pubitemid 128428054)
4. Brody EN, et al. (1995) Old phage, new insights: Two recently recognized mechanisms of transcriptional regulation in bacteriophage T4 development. FEMS MIcrobiol Lett 128:1-8.
5. Herendeen DR, Williams KP, Kassavetis GA, Geiduschek EP (1990) An RNA polymerasebinding protein that is required for communication between an enhancer and a promoter. Science 278:573-578.
6. Geiduschek EP, Kassavetis GA (2010) Transcription of the T4 late genes. Virol J 7:288-300.
7. Sanders GM, Kassavetis GA, Geiduschek EP (1997) Dual targets of a transriptional activator that tracks on DNA. EMBO J 16:3124-3132. (Pubitemid 27234952)
8. Wong K, Geiduschek EP (1998) Activator-sigma interaction: a hydrophobic segment mediates the interaction of a sigma family promoter recognition protein with a sliding clamp transcription activator. J Mol Biol 284:195-203. (Pubitemid 28542448)
9. Gribskov M, Burgess RR (1986) Sigma factors from E coli, B. subtilis, phage SPO1, and phage T4 are homologous proteins. Nucleic Acids Res 14:6745-6763.
10. 70 family: Sequence conservation and evolutionary relationships. J Bacteriol 174:3843-3849.
11. Lane WJ, Darst SA (2010) Molecular evolution of multi-subunit RNA polymerases: structural analysis. J Mol Biol 395:686-704.
12. Wong K, Kassavetis GA, Leonetti J-P, Geiduschek EP (2003) Mutational and functional analysis of a segment of the sigma family bacteriophage T4 late promoter recognition protein gp55. J Biol Chem 278:7073-7080. (Pubitemid 36800704)
13. Kassavetis GA, Geiduschek EP (1984) Defining a bacteriophage T4 late promoter: bacteriophage T4 gene 55 protein suffices for directing late promoter recognition. Proc Natl Acad Sci USA 81:5101-5105. (Pubitemid 14008888)
14. Christensen AC, Young ET (1982) T4 late transcripts are initiated near a conserved DNA sequence. Nature 299:369-371. (Pubitemid 12012870)
15. Nechaev S, Kamali-Moghaddam M, Andre E, Leonetti J-P, Geiduschek EP (2004) The bacteriophage T4 late-transcription coactivator gp33 binds the flap domain of Escherichia coli RNA polymerase. Proc Natl Acad Sci USA 101:17365-17370. (Pubitemid 39657410)
16. Williams KP, Muller R, RugerW, Geiduschek EP (1989) Overproduced bacteriophage T4 gene 33 protein binds RNA polymerase. J Bacteriol 171:3579-3582. (Pubitemid 19145721)
17. Kolesky SE, Ouhammouch M, Geiduschek EP (2002) The mechanism of transcriptional activation by the topologically DNA-linked sliding clamp of bacteriophage T4. J Mol Biol 321:767-784.
18. Riva S, Cascino A, Geiduschek EP (1970) Coupling of late transcription to viral replication in bacteriophage T4 development. J Mol Biol 54:85-102.
19. Lewin B (1990) Commitment and activation at pol II promoters: a tail of proteinprotein interactions. Cell 61:1161-1164.
20. F, contacting multiple conserved regions of the σ factor. J Mol Biol 300:17-28.
21. Hendrickson W, Norton JR, LeMaster DM (1990) Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD). EMBO J 9:1665-1672.
22. Lane WJ, Darst SA (2010) Molecular evolution of multi-subunit RNA polymerases: sequence analysis. J Mol Biol 395:671-685.
23. Opalka N, et al. (2010) Complete structural model of Escherichia coli RNA polymerase from a hybrid approach. PLoS Biol 8:e1000483.
24. Zhang G, et al. (1999) Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell 98:811-824.
25. Vassylyev DG, et al. (2002) Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature 417:712-719. (Pubitemid 34640620)
26. Kuznedelov K, et al. (2006) RecombinantThermus aquaticus RNA polymerase for structural studies. J Mol Biol 359:110-121.
27. Kuznedelov K, et al. (2002) A role for interaction of the RNA polymerase flap domain with the sigma subunit in promoter recognition. Science 295:855-857. (Pubitemid 34118366)
28. Campbell EA, et al. (2002) Structure of the bacterial RNA polymerase promoter specificity sigma factor. Mol Cell 9:527-539. (Pubitemid 34273784)
29. Nechaev S, Geiduschek EP (2006) The role of an upstream promoter interaction in initiation of bacterial transcription. EMBO J 25:1700-1709.
30. Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402. (Pubitemid 27359211)
31. Landau M, et al. (2005) ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 33:W299-W302. (Pubitemid 44529930)
32. Geszvain K, Gruber TM, Mooney RA, Gross CA, Landick R (2004) A hydrophobic patch on the flap-tip helix of E. coli RNA polymerase mediates ó70 region 4 function. J Mol Biol 343:569-587. (Pubitemid 39311606)
33. Dove SL, Hochschild A (2004) A bacterial two-hybrid system based on transcription activation. Methods in Molecular Biology 261:231-246.
34. Shamoo Y, Steitz TA (1999) Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex. Cell 99:155-166. (Pubitemid 29491782)
35. Tinker RL, Sanders GM, Severinov K, Kassavetis GA, Geiduschek EP (1995) The COOH-terminal domain of the RNA polymerase a subunit in transcriptional enhancement and deactivation at the bacteriophage T4 late promoter. J Biol Chem 270:15899-15907.
36. Tinker RL, Williams KP, Kassavetis GA, Geiduschek EP (1994) Transcriptional activation by a DNA-tracking protein: structural consequences of enhancement at the T4 late promoter. Cell 77:225-237. (Pubitemid 24138620)
37. Nechaev S, Geiduschek EP (2008) Dissection of the bacteriophage T4 late promoter complex. J Mol Biol 379:402-413.
38. 70 and the σ-flap of Escherichia coli RNA polymerase inhibits extension of nascent RNA during early elongation. Proc Natl Acad Sci USA 102:4488-4493.
39. 70 region 4/β flap interaction facilitates engagement of RNA polymerase by the Q antiterminator. Mol Cell 24:457-468.
40. Vassylyev DG, Vassylyeva MN, Perederina A, Tahirov TH, Artsimovitch I (2007) Structural basis for transcription elongation by bacterial RNA polymerase. Nature 448:157-162. (Pubitemid 47067370)
41. Epstein RH, et al. (1963) Physiological studies of conditional lethal mutants of bacteriophage T4D. Cold Spring Harbor Symp Quant Biol 28:375-394.
42. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc Natl Acad Sci USA 98:10037-10041. (Pubitemid 32802969)