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 Mg2+ and positions it for catalysis.
“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
RNA polymerase enzymes solve the problems of metal ion catalysis by binding and precisely positioning the metal ion for catalysis.
“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
Multi-subunit cellular RNA polymerases use two Mg2+ ions, with the more tightly bound ion coordinated to three asp residues in a conserved NADFDGD sequence.
“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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Structure of paused transcription complex Pol II–DSIF–NELF
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Self-citationPrebiotic Peptides: Molecular Hubs in the Origin of Life
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The RNA polymerase III transcription apparatus11Edited by P. E. Wright
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A structural perspective of CTD functionPreprint
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Self-citationArchitecture of the RNA Polymerase II-TFIIS Complex and Implications for mRNA Cleavage
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Self-citationStructural Basis for the Transition from Initiation to Elongation Transcription in T7 RNA Polymerase
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A ratchet mechanism of transcription elongation and its control.
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Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms
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Transcriptional regulation and the role of diverse coactivators in animal cells
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Protocells and RNA Self-Replication
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Structural systems biology: modelling protein interactions
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Advances in bacterial promoter recognition and its control by factors that do not bind DNA
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Structural Basis of Transcription
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Self-citationRNA polymerase II–TFIIB structure and mechanism of transcription initiation
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Self-citationOn the importance of being co-transcriptional
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Structural basis of transcription: α-Amanitin–RNA polymerase II cocrystal at 2.8 Å resolution
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Self-citationRecognition of RNA polymerase II carboxy-terminal domain by 3′-RNA-processing factors
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Self-citationArchitecture of the RNA polymerase II–Mediator core initiation complex
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Bacterial Transcription Terminators: The RNA 3′-End Chronicles
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Structure of Eukaryotic RNA Polymerases
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Self-citationRapid evolution of silver nanoparticle resistance in Escherichia coli
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Unravelling the means to an end: RNA polymerase II transcription termination
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Self-citationStructure and mechanism of the RNA polymerase II transcription machineryPreprint
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Transitions in RNA polymerase II elongation complexes at the 3′ ends of genes
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Self-citationStructural Basis for Transcription Regulation by Alarmone ppGpp
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Intrinsically unstructured proteins evolve by repeat expansion
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The RNA Polymerase II Machinery
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Architecture of initiation-competent 12-subunit RNA polymerase II
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Self-citationTranscription initiation complex structures elucidate DNA opening
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SYMMETRY, FORM, AND SHAPE: Guiding Principles for Robustness in Macromolecular Machines
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Structures of transcription pre-initiation complex with TFIIH and Mediator
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Self-citationThe mRNA assembly line: transcription and processing machines in the same factory
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The RNA Polymerase II Elongation Complex
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Self-citationThe regulatory roles and mechanism of transcriptional pausing
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Nascent RNA analyses: tracking transcription and its regulation
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The development and characterization of synthetic minimal yeast promoters
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Self-citationStructure of a T7 RNA polymerase elongation complex at 2.9 Å resolution
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Structures of Complete RNA Polymerase II and Its Subcomplex, Rpb4/7
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Architecture of the RNA polymerase–Spt4/5 complex and basis of universal transcription processivity
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Opening and Closing of the Bacterial RNA Polymerase Clamp
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- 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
- Physical Sciences › Materials Science › Materials Chemistry › 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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