Crystal Structure of Thermus aquaticus Core RNA Polymerase at 3.3 Å Resolution
Open accessAbstract
The X-ray crystal structure of Thermus aquaticus core RNA polymerase reveals a "crab claw"-shaped molecule with a 27 A wide internal channel. Located on the back wall of the channel is a Mg2+ ion required for catalytic activity, which is chelated by an absolutely conserved motif from all bacterial and eukaryotic cellular RNA polymerases. The structure places key functional sites, defined by mutational and cross-linking analysis, on the inner walls of the channel in close proximity to the active center Mg2+. Further out from the catalytic center, structural features are found that may be involved in maintaining the melted transcription bubble, clamping onto the RNA product and/or DNA template to assure processivity, and delivering nucleotide substrates to the active center.
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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 Zhang et al. 1999
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 Zhang et al. 1999
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 [60]
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- Authors
- Zhang, G., Campbell, E. A., Minakhin, L., Richter, C., Severinov, K., & Darst, S. A.
- Affiliations
- Rockefeller University (US)
- Rutgers, The State University of New Jersey (US)
- Corresponding author
- Darst, Seth A
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 1999-09
- Volume
- 98
- Issue
- 6
- Pages
- 811-824
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2107870109
- Cited by
- 813
- References
- 0
- Citations by year
- 2026: 12 · 2025: 12 · 2024: 19 · 2023: 10 · 2022: 7 · 2021: 20 · 2020: 16 · 2019: 28 · 2018: 21 · 2017: 23 · 2016: 15 · 2015: 21 · 2014: 29 · 2013: 25 · 2012: 24
- FWCI
- 49.65
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (5f32gm019441-02)
- National Institute of General Medical Sciences (GM 19441-01)
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- Thermus aquaticus, core RNA polymerase, transcription initiation, internal channels, active site, transcription bubble, processivity, archaeal RNA polymerase
- MeSH terms
- Chloroplasts, Cloning, Molecular, Cross-Linking Reagents, DNA Mutational Analysis, Gene Expression Regulation, Models, Molecular, Nucleotides, Prokaryotic Cells, DNA-Directed RNA Polymerases, Structure-Activity Relationship, Thermus, Transcription, Genetic, Reproducibility of Results, Sequence Analysis, DNA, Protein Structure, Secondary, Crystallography, X-Ray, Catalytic Domain
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