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Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution
Open accessAbstract
Structures of a 10-subunit yeast RNA polymerase II have been derived from two crystal forms at 2.8 and 3.1 angstrom resolution. Comparison of the structures reveals a division of the polymerase into four mobile modules, including a clamp, shown previously to swing over the active center. In the 2.8 angstrom structure, the clamp is in an open state, allowing entry of straight promoter DNA for the initiation of transcription. Three loops extending from the clamp may play roles in RNA unwinding and DNA rewinding during transcription. A 2.8 angstrom difference Fourier map reveals two metal ions at the active site, one persistently bound and the other possibly exchangeable during RNA synthesis. The results also provide evidence for RNA exit in the vicinity of the carboxyl-terminal repeat domain, coupling synthesis to RNA processing by enzymes bound to this domain.
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“A short acidic peptide in the active site of cellular RNA polymerase binds Mg 2+ and positions it for catalysis (Zhang et al. 1999;Cramer et al. 2001).”
From Protocells and RNA Self-Replication (2018) · cites this paper as Cramer et al. 2001
In the citing paper
“RNA polymerase enzymes solve these problems by binding and precisely positioning the metal ion for catalysis (Zhang et al. 1999;Cramer et al. 2001;Robertson and Scott 2007;Shechner et al. 2009).”
From Protocells and RNA Self-Replication (2018) · cites this paper as Cramer et al. 2001
In the citing paper
“Interestingly, the multi-subunit cellular RNA polymerases also use two Mg 2+ ions in the active site, of which the more tightly bound ion is coordinated to three asp residues in a highly conserved NADFDGD peptide sequence [60,61].”
From The eightfold path to non-enzymatic RNA replication (2012) · cites this paper as [61]
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Self-citationKuznetsova, A. V., Meller, J., Schnell, P. O., Nash, J. A., Ignacak, M. L., Sánchez, Y., Conaway, J. W., Conaway, R. C., & Czyzyk-Krzeska, M. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0436037100 · Cited by 230
Opening and Closing of the Bacterial RNA Polymerase Clamp
Chakraborty, A., Wang, D., Ebright, Y. W., Korlann, Y., Kortkhonjia, E., Kim, T., Chowdhury, S., Wigneshweraraj, S., Irschik, H., Jansen, R., et al. (2012) · Science · doi:10.1126/science.1218716 · Cited by 230
Metadata
- Authors
- Cramer, P., Bushnell, D. A., & Kornberg, R. D.
- Affiliations
- Stanford Medicine (US)
- Corresponding author
- Cramer, Patrick
- Kornberg, Roger D.
- Venue
- Science
- Published
- 2001-06-08
- Volume
- 292
- Issue
- 5523
- Pages
- 1863-1876
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2074206760
- Cited by
- 1,247
- References
- 71
- Citations by year
- 2026: 18 · 2025: 16 · 2024: 40 · 2023: 29 · 2022: 29 · 2021: 38 · 2020: 38 · 2019: 48 · 2018: 34 · 2017: 51 · 2016: 33 · 2015: 37 · 2014: 50 · 2013: 55 · 2012: 63
- FWCI
- 27.00
- Type
- journal article
- Language
- en
- Open access
- green
- hdl.handle.net
- Licence
- other-oa
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Max Planck Digital Library (submittedVersion, other-oa)
- GRO (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Funders
- National Institute of General Medical Sciences (GM49985, R01GM049985)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- RNA polymerase II, transcription initiation, active site metal ions, RNA unwinding, promoter DNA, crystal structure
- MeSH terms
- Amino Acid Sequence, Binding Sites, DNA, Fungal, Fourier Analysis, Hydrogen Bonding, Magnesium, Metals, Models, Molecular, Molecular Sequence Data, Promoter Regions, Genetic, Protein Conformation, RNA Polymerase II, RNA Processing, Post-Transcriptional, RNA, Fungal, RNA, Messenger, Saccharomyces cerevisiae, Transcription Factors, Transcription, Genetic, Conserved Sequence, Protein Structure, Secondary, Protein Structure, Tertiary, Crystallography, X-Ray, Protein Structure, Quaternary, Protein Subunits
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