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  • 1
    Publication Date: 2011-12-14
    Description: Activated transcription of the bacteriophage T4 late genes, which is coupled to concurrent DNA replication, is accomplished by an initiation complex containing the host RNA polymerase associated with two phage-encoded proteins, gp55 (the basal promoter specificity factor) and gp33 (the coactivator), as well as the DNA-mounted sliding-clamp processivity factor of the phage T4 replisome (gp45, the activator). We have determined the 3.0 Å-resolution X-ray crystal structure of gp33 complexed with its RNA polymerase binding determinant, the β-flap domain. Like domain 4 of the promoter specificity σ factor (σ4), gp33 interacts with RNA polymerase primarily by clamping onto the helix at the tip of the β-flap domain. Nevertheless, gp33 and σ4 are not structurally related. The gp33/β-flap structure, combined with biochemical, biophysical, and structural information, allows us to generate a structural model of the T4 late promoter initiation complex. The model predicts protein/protein interactions within the complex that explain the presence of conserved patches of surface-exposed residues on gp33, and provides a structural framework for interpreting and designing future experiments to functionally characterize the complex.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 2
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1998-07-10
    Description: The 2.5 angstrom resolution x-ray crystal structure of the Escherichia coli RNA polymerase (RNAP) alpha subunit amino-terminal domain (alphaNTD), which is necessary and sufficient to dimerize and assemble the other RNAP subunits into a transcriptionally active enzyme and contains all of the sequence elements conserved among eukaryotic alpha homologs, has been determined. The alphaNTD monomer comprises two distinct, flexibly linked domains, only one of which participates in the dimer interface. In the alphaNTD dimer, a pair of helices from one monomer interact with the cognate helices of the other to form an extensive hydrophobic core. All of the determinants for interactions with the other RNAP subunits lie on one face of the alphaNTD dimer. Sequence alignments, combined with secondary-structure predictions, support proposals that a heterodimer of the eukaryotic RNAP subunits related to Saccharomyces cerevisiae Rpb3 and Rpb11 plays the role of the alphaNTD dimer in prokaryotic RNAP.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, G -- Darst, S A -- GM19441-01/GM/NIGMS NIH HHS/ -- GM53759/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Jul 10;281(5374):262-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9657722" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; DNA-Directed RNA Polymerases/*chemistry ; Dimerization ; Escherichia coli/*enzymology ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; RNA Polymerase II/chemistry ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2000-08-01
    Description: The path of the nucleic acids through a transcription elongation complex was tracked by mapping cross-links between bacterial RNA polymerase (RNAP) and transcript RNA or template DNA onto the x-ray crystal structure. In the resulting model, the downstream duplex DNA is nestled in a trough formed by the beta' subunit and enclosed on top by the beta subunit. In the RNAP channel, the RNA/DNA hybrid extends from the enzyme active site, along a region of the beta subunit harboring rifampicin resistance mutations, to the beta' subunit "rudder." The single-stranded RNA is then extruded through another channel formed by the beta-subunit flap domain. The model provides insight into the functional properties of the transcription complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korzheva, N -- Mustaev, A -- Kozlov, M -- Malhotra, A -- Nikiforov, V -- Goldfarb, A -- Darst, S A -- GM30717/GM/NIGMS NIH HHS/ -- GM49242/GM/NIGMS NIH HHS/ -- GM53759/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Jul 28;289(5479):619-25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Public Health Research Institute, 455 First Avenue, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10915625" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cross-Linking Reagents ; Crystallography, X-Ray ; DNA/chemistry/genetics/*metabolism ; DNA Primers ; DNA-Directed RNA Polymerases/*chemistry/genetics/metabolism ; Models, Molecular ; Mutation ; Nucleic Acid Conformation ; Nucleic Acid Hybridization ; Oligodeoxyribonucleotides/chemistry/metabolism ; Oligoribonucleotides/chemistry/metabolism ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Messenger/chemistry/genetics/*metabolism ; Templates, Genetic ; Thermus/enzymology ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2002-05-23
    Description: The crystal structure of the initiating form of Thermus aquaticus RNA polymerase, containing core RNA polymerase (alpha2betabeta'omega) and the promoter specificity sigma subunit, has been determined at 4 angstrom resolution. Important structural features of the RNA polymerase and their roles in positioning sigma within the initiation complex are delineated, as well as the role played by sigma in modulating the opening of the RNA polymerase active-site channel. The two carboxyl-terminal domains of sigma are separated by 45 angstroms on the surface of the RNA polymerase, but are linked by an extended loop. The loop winds near the RNA polymerase active site, where it may play a role in initiating nucleotide substrate binding, and out through the RNA exit channel. The advancing RNA transcript must displace the loop, leading to abortive initiation and ultimately to sigma release.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murakami, Katsuhiko S -- Masuda, Shoko -- Darst, Seth A -- GM53759/GM/NIGMS NIH HHS/ -- GM61898/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 May 17;296(5571):1280-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12016306" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA, Bacterial/metabolism ; DNA-Directed RNA Polymerases/*chemistry/*metabolism ; Eukaryotic Cells/metabolism ; Holoenzymes/chemistry/metabolism ; Models, Molecular ; Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Bacterial/metabolism ; RNA, Messenger/metabolism ; Sigma Factor/metabolism ; Thermus/*enzymology ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2002-05-23
    Description: The crystal structure of Thermus aquaticus RNA polymerase holoenzyme (alpha2betabeta'omegasigmaA) complexed with a fork-junction promoter DNA fragment has been determined by fitting high-resolution x-ray structures of individual components into a 6.5-angstrom resolution map. The DNA lies across one face of the holoenzyme, completely outside the RNA polymerase active site channel. All sequence-specific contacts with core promoter elements are mediated by the sigma subunit. A universally conserved tryptophan is ideally positioned to stack on the exposed face of the base pair at the upstream edge of the transcription bubble. Universally conserved basic residues of the sigma subunit provide critical contacts with the DNA phosphate backbone and play a role in directing the melted DNA template strand into the RNA polymerase active site. The structure explains how holoenzyme recognizes promoters containing variably spaced -10 and -35 elements and provides the basis for models of the closed and open promoter complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murakami, Katsuhiko S -- Masuda, Shoko -- Campbell, Elizabeth A -- Muzzin, Oriana -- Darst, Seth A -- GM20470/GM/NIGMS NIH HHS/ -- GM53759/GM/NIGMS NIH HHS/ -- GM61898/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 May 17;296(5571):1285-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12016307" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA, Bacterial/*chemistry/genetics/metabolism ; DNA-Directed RNA Polymerases/*chemistry/metabolism ; Holoenzymes/chemistry/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; *Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Subunits ; Sigma Factor/*chemistry/metabolism ; Templates, Genetic ; Thermus/*enzymology ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2012-09-11
    Description: Transcription-coupled DNA repair uses components of the transcription machinery to identify DNA lesions and initiate their repair. These repair pathways are complex, so their mechanistic features remain poorly understood. Bacterial transcription-coupled repair is initiated when RNA polymerase stalled at a DNA lesion is removed by Mfd, an ATP-dependent DNA translocase. Here we use single-molecule DNA nanomanipulation to observe the dynamic interactions of Escherichia coli Mfd with RNA polymerase elongation complexes stalled by a cyclopyrimidine dimer or by nucleotide starvation. We show that Mfd acts by catalysing two irreversible, ATP-dependent transitions with different structural, kinetic and mechanistic features. Mfd remains bound to the DNA in a long-lived complex that could act as a marker for sites of DNA damage, directing assembly of subsequent DNA repair factors. These results provide a framework for considering the kinetics of transcription-coupled repair in vivo, and open the way to reconstruction of complete DNA repair pathways at single-molecule resolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3475728/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3475728/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Howan, Kevin -- Smith, Abigail J -- Westblade, Lars F -- Joly, Nicolas -- Grange, Wilfried -- Zorman, Sylvain -- Darst, Seth A -- Savery, Nigel J -- Strick, Terence R -- BB/I001859/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/I003142/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- GM073829/GM/NIGMS NIH HHS/ -- R01 GM073829/GM/NIGMS NIH HHS/ -- England -- Nature. 2012 Oct 18;490(7420):431-4. doi: 10.1038/nature11430. Epub 2012 Sep 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut Jacques Monod, CNRS, UMR 7592, University Paris Diderot, Sorbonne Paris Cite F-75205 Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22960746" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Bacterial Proteins/*metabolism ; Biocatalysis ; DNA Damage ; *DNA Repair ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli/enzymology/genetics/metabolism ; Hydrolysis ; Kinetics ; Promoter Regions, Genetic/genetics ; Pyrimidine Dimers/chemistry/metabolism ; Transcription Elongation, Genetic ; Transcription Factors/*metabolism ; Transcription Initiation, Genetic ; Transcription Termination, Genetic ; *Transcription, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2010-05-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gleick, P H -- Adams, R M -- Amasino, R M -- Anders, E -- Anderson, D J -- Anderson, W W -- Anselin, L E -- Arroyo, M K -- Asfaw, B -- Ayala, F J -- Bax, A -- Bebbington, A J -- Bell, G -- Bennett, M V L -- Bennetzen, J L -- Berenbaum, M R -- Berlin, O B -- Bjorkman, P J -- Blackburn, E -- Blamont, J E -- Botchan, M R -- Boyer, J S -- Boyle, E A -- Branton, D -- Briggs, S P -- Briggs, W R -- Brill, W J -- Britten, R J -- Broecker, W S -- Brown, J H -- Brown, P O -- Brunger, A T -- Cairns, J Jr -- Canfield, D E -- Carpenter, S R -- Carrington, J C -- Cashmore, A R -- Castilla, J C -- Cazenave, A -- Chapin, F S 3rd -- Ciechanover, A J -- Clapham, D E -- Clark, W C -- Clayton, R N -- Coe, M D -- Conwell, E M -- Cowling, E B -- Cowling, R M -- Cox, C S -- Croteau, R B -- Crothers, D M -- Crutzen, P J -- Daily, G C -- Dalrymple, G B -- Dangl, J L -- Darst, S A -- Davies, D R -- Davis, M B -- De Camilli, P V -- Dean, C -- DeFries, R S -- Deisenhofer, J -- Delmer, D P -- DeLong, E F -- DeRosier, D J -- Diener, T O -- Dirzo, R -- Dixon, J E -- Donoghue, M J -- Doolittle, R F -- Dunne, T -- Ehrlich, P R -- Eisenstadt, S N -- Eisner, T -- Emanuel, K A -- Englander, S W -- Ernst, W G -- Falkowski, P G -- Feher, G -- Ferejohn, J A -- Fersht, A -- Fischer, E H -- Fischer, R -- Flannery, K V -- Frank, J -- Frey, P A -- Fridovich, I -- Frieden, C -- Futuyma, D J -- Gardner, W R -- Garrett, C J R -- Gilbert, W -- Goldberg, R B -- Goodenough, W H -- Goodman, C S -- Goodman, M -- Greengard, P -- Hake, S -- Hammel, G -- Hanson, S -- Harrison, S C -- Hart, S R -- Hartl, D L -- Haselkorn, R -- Hawkes, K -- Hayes, J M -- Hille, B -- Hokfelt, T -- House, J S -- Hout, M -- Hunten, D M -- Izquierdo, I A -- Jagendorf, A T -- Janzen, D H -- Jeanloz, R -- Jencks, C S -- Jury, W A -- Kaback, H R -- Kailath, T -- Kay, P -- Kay, S A -- Kennedy, D -- Kerr, A -- Kessler, R C -- Khush, G S -- Kieffer, S W -- Kirch, P V -- Kirk, K -- Kivelson, M G -- Klinman, J P -- Klug, A -- Knopoff, L -- Kornberg, H -- Kutzbach, J E -- Lagarias, J C -- Lambeck, K -- Landy, A -- Langmuir, C H -- Larkins, B A -- Le Pichon, X T -- Lenski, R E -- Leopold, E B -- Levin, S A -- Levitt, M -- Likens, G E -- Lippincott-Schwartz, J -- Lorand, L -- Lovejoy, C O -- Lynch, M -- Mabogunje, A L -- Malone, T F -- Manabe, S -- Marcus, J -- Massey, D S -- McWilliams, J C -- Medina, E -- Melosh, H J -- Meltzer, D J -- Michener, C D -- Miles, E L -- Mooney, H A -- Moore, P B -- Morel, F M M -- Mosley-Thompson, E S -- Moss, B -- Munk, W H -- Myers, N -- Nair, G B -- Nathans, J -- Nester, E W -- Nicoll, R A -- Novick, R P -- O'Connell, J F -- Olsen, P E -- Opdyke, N D -- Oster, G F -- Ostrom, E -- Pace, N R -- Paine, R T -- Palmiter, R D -- Pedlosky, J -- Petsko, G A -- Pettengill, G H -- Philander, S G -- Piperno, D R -- Pollard, T D -- Price, P B Jr -- Reichard, P A -- Reskin, B F -- Ricklefs, R E -- Rivest, R L -- Roberts, J D -- Romney, A K -- Rossmann, M G -- Russell, D W -- Rutter, W J -- Sabloff, J A -- Sagdeev, R Z -- Sahlins, M D -- Salmond, A -- Sanes, J R -- Schekman, R -- Schellnhuber, J -- Schindler, D W -- Schmitt, J -- Schneider, S H -- Schramm, V L -- Sederoff, R R -- Shatz, C J -- Sherman, F -- Sidman, R L -- Sieh, K -- Simons, E L -- Singer, B H -- Singer, M F -- Skyrms, B -- Sleep, N H -- Smith, B D -- Snyder, S H -- Sokal, R R -- Spencer, C S -- Steitz, T A -- Strier, K B -- Sudhof, T C -- Taylor, S S -- Terborgh, J -- Thomas, D H -- Thompson, L G -- Tjian, R T -- Turner, M G -- Uyeda, S -- Valentine, J W -- Valentine, J S -- Van Etten, J L -- van Holde, K E -- Vaughan, M -- Verba, S -- von Hippel, P H -- Wake, D B -- Walker, A -- Walker, J E -- Watson, E B -- Watson, P J -- Weigel, D -- Wessler, S R -- West-Eberhard, M J -- White, T D -- Wilson, W J -- Wolfenden, R V -- Wood, J A -- Woodwell, G M -- Wright, H E Jr -- Wu, C -- Wunsch, C -- Zoback, M L -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 May 7;328(5979):689-90. doi: 10.1126/science.328.5979.689.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20448167" target="_blank"〉PubMed〈/a〉
    Keywords: *Climate Change ; Politics ; Public Policy ; Research/standards ; Research Personnel
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2006-10-30
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 9
    Publication Date: 1998-07-07
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 10
    Publication Date: 1990-03-01
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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