The DOI matches its Crossref record; 26 of the 26 references it cites were found in a registry or an index.
Structural Basis of Transcription Initiation: An RNA Polymerase Holoenzyme-DNA Complex
Abstract
The crystal structure of Thermus aquaticus RNA polymerase holoenzyme (α 2 ββ′ωσ A ) 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 σ 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 σ 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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Jones, T. A., Zou, J. Y., Cowan, S. W., & Kjeldgaard, M. (1991) · Acta Crystallographica Section A Foundations of Crystallography · doi:10.1107/s0108767390010224 · Cited by 12,648
Nicholls, A., Sharp, K. A., & Honig, B. (1991) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340110407 · Cited by 5,240
Structural Mechanism for Rifampicin Inhibition of Bacterial RNA Polymerase
Campbell, E. A., Korzheva, N., Mustaev, A., Murakami, K., Nair, S., Goldfarb, A., & Darst, S. A. (2001) · Cell · doi:10.1016/s0092-8674(01)00286-0 · Cited by 1,556
Self-citationLavery, R., & Sklenar, H. (1988) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.1988.10506483 · Cited by 894
The sigma 70 family: sequence conservation and evolutionary relationships
Lonetto, M., Gribskov, M., & Gross, C. A. (1992) · Journal of Bacteriology · doi:10.1128/jb.174.12.3843-3849.1992 · Cited by 888
Crystal Structure of Thermus aquaticus Core RNA Polymerase at 3.3 Å Resolution
Zhang, G., Campbell, E. A., Minakhin, L., Richter, C., Severinov, K., & Darst, S. A. (1999) · Cell · doi:10.1016/s0092-8674(00)81515-9 · Cited by 813
Self-citationCarson, M. (1991) · Journal of Applied Crystallography · doi:10.1107/s0021889891007240 · Cited by 808
Structural Basis of Transcription Initiation: RNA Polymerase Holoenzyme at 4 Å Resolution
Murakami, K. S., Masuda, S., & Darst, S. A. (2002) · Science · doi:10.1126/science.1069594 · Cited by 541
Self-citationStructure of the Bacterial RNA Polymerase Promoter Specificity σ Subunit
Campbell, E. A., Muzzin, O., Chlenov, M., Sun, J. L., Olson, C. A., Weinman, O., Trester-Zedlitz, M. L., & Darst, S. A. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00470-7 · Cited by 491
Self-citationThe Functional and Regulatory Roles of Sigma Factors in Transcription
GROSS, C. A., CHAN, C., DOMBROSKI, A., GRUBER, T., SHARP, M., TUPY, J., & YOUNG, B. (1998) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1998.63.141 · Cited by 366
RNA Polymerase-Promoter Interactions: the Comings and Goings of RNA Polymerase
deHaseth, P. L., Zupancic, M. L., & Record, M. T. (1998) · Journal of Bacteriology · doi:10.1128/jb.180.12.3019-3025.1998 · Cited by 291
Barne, K. A., Bown, J. A., Busby, S. J. W., & Minchin, S. D. (1997) · The EMBO Journal · doi:10.1093/emboj/16.13.4034 · Cited by 272
Gourse, R. L., Ross, W., & Gaal, T. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.01972.x · Cited by 270
X-ray structure of the DNase I-d(GGTATACC)2 complex at 2·3Å resolution
Weston, S. A., Lahm, A., & Suck, D. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)91064-v · Cited by 248
Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase
Harada, Y., Ohara, O., Takatsuki, A., Itoh, H., Shimamoto, N., & Kinosita, K. (2001) · Nature · doi:10.1038/35051126 · Cited by 235
Transcription Processivity: Protein-DNA Interactions Holding Together the Elongation Complex
Nudler, E., Avetissova, E., Markovtsov, V. V., & Goldfarb, A. (1996) · Science · doi:10.1126/science.273.5272.211 · Cited by 194
The Escherichia coli RNA polymerase α subunit: structure and function
Ebright, R. H., & Busby, S. (1995) · Current Opinion in Genetics & Development · doi:10.1016/0959-437x(95)80008-5 · Cited by 162
Topography of intermediates in transcription initiation of E.coli.
Schickor, P., Metzger, W., Werel, W., Lederer, H., & Heumann, H. (1990) · The EMBO Journal · doi:10.1002/j.1460-2075.1990.tb07391.x · Cited by 140
Molecular systematic studies of eubacteria, using sigma70-type sigma factors of group 1 and group 2
Gruber, T. M., & Bryant, D. A. (1997) · Journal of Bacteriology · doi:10.1128/jb.179.5.1734-1747.1997 · Cited by 136
Ross, W., Ernst, A., & Gourse, R. L. (2001) · Genes & Development · doi:10.1101/gad.870001 · Cited by 113
A cinematographic view of Escherichia coli RNA polymerase translocation.
Metzger, W., Schickor, P., & Heumann, H. (1989) · The EMBO Journal · doi:10.1002/j.1460-2075.1989.tb08416.x · Cited by 108
Young, B. A., Anthony, L. C., Gruber, T. M., Arthur, T. M., Heyduk, E., Lu, C. Z., Sharp, M. M., Heyduk, T., Burgess, R. R., & Gross, C. A. (2001) · Cell · doi:10.1016/s0092-8674(01)00398-1 · Cited by 97
Craig, M. L., Suh, W.-C., & Record, M. T. (1995) · Biochemistry · doi:10.1021/bi00048a004 · Cited by 95
Jeon, Y. H., Yamazaki, T., Otomo, T., Ishihama, A., & Kyogoku, Y. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.0902 · Cited by 77
Cowing, D. W., Mecsas, J. C., Record, M. T., & Gross, C. A. (1989) · Journal of Molecular Biology · doi:10.1016/0022-2836(89)90128-9 · Cited by 75
Development of RNA polymerase-promoter contacts during open complex formation
Mecsas, J. C., Cowing, D. W., & Gross, C. A. (1991) · Journal of Molecular Biology · doi:10.1016/0022-2836(91)90102-c · Cited by 57
Cited by
The regulation of bacterial transcription initiation
Browning, D. F., & Busby, S. J. W. (2004) · Nature Reviews Microbiology · doi:10.1038/nrmicro787 · Cited by 1,019
Evolution of multisubunit RNA polymerases in the three domains of life
Werner, F., & Grohmann, D. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2507 · Cited by 431
rRNA Transcription in Escherichia coli
Paul, B. J., Ross, W., Gaal, T., & Gourse, R. L. (2004) · Annual Review of Genetics · doi:10.1146/annurev.genet.38.072902.091347 · Cited by 336
Advances in bacterial promoter recognition and its control by factors that do not bind DNA
Haugen, S. P., Ross, W., & Gourse, R. L. (2008) · Nature Reviews Microbiology · doi:10.1038/nrmicro1912 · Cited by 320
Kaplan, C. D., Larsson, K.-M., & Kornberg, R. D. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.04.023 · Cited by 246
Metadata
- Authors
- Murakami, K. S., Masuda, S., Campbell, E. A., Muzzin, O., & Darst, S. A.
- Venue
- Science
- Published
- 2002-05-17
- Volume
- 296
- Issue
- 5571
- Pages
- 1285-1290
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2143641256
- Cited by
- 641
- References
- 26
- FWCI
- 19.87
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
