DNA Lesion Bypass Polymerases Open Up
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Structures of catalytic fragments of two DNA lesion bypass DNA polymerases, yeast DNA polymerase eta and an archeon DinB homolog, have recently been solved. These structures share several common architectural and structural features observed in other DNA polymerases, including a hand-like architecture with fingers, palm, and thumb subdomains. The new structures provide the first structural insights into DNA lesion bypass. The fingers and thumb are smaller than those in other DNA polymerases. Modeled substrates suggest that the fingers in the vicinity of the incoming nucleotide is closed, a conformation not previously observed for an unliganded polymerase. However, the template binding pocket appears to be more open, indicating that for DNA polymerase eta, a covalently linked thymine-thymine dimer could be accommodated.
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Crystal structures reveal that polymerase binding to DNA strongly reshapes the primer-template, for example the backbone at the templating base can be bent by 90°.
“Crystal structures (Refs.15-22 and references therein) reveal that polymerase binding to DNA strongly reshapes the primertemplate, e.g. the backbone at the templating base can be bent by 90°.”
From DNA Replication Fidelity (2004) · cites this paper as [21]
These ideas are supported by structural information and by a report that the insertion fidelity of yeast Pol η is severely impaired with difluorotoluene, a nonpolar isosteric analog of thymine that is unable to form Watson-Crick hydrogen bonds with adenine.
“These ideas are supported by structural information (20, 21, 26 -28) and by a report (29) that the insertion fidelity of yeast Pol is severely impaired with difluorotoluene, a nonpolar isosteric analog of thymine that is unable to form Watson-Crick hydrogen bonds with adenine.”
From DNA Replication Fidelity (2004) · cites this paper as [21]
Certain Y family polymerases are suggested to be in a closed conformation without dNTP, yet kinetic data have emphasized the importance of a dNTP-induced conformational change preceding chemistry to the fidelity of Pol η.
“Moreover, certain Y family polymerases are suggested to be in a closed conformation without dNTP (Refs.20 and 21 but also see comments in Ref. 28), yet kinetic data (40) have emphasized the importance of a dNTP-induced conformational change preceding chemistry to the fidelity of Pol .”
From DNA Replication Fidelity (2004) · cites this paper as [21]
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- Authors
- Beard, W. A., & Wilson, S. H.
- Affiliations
- National Institute of Environmental Health Sciences (US)
- National Institutes of Health (US)
- Corresponding author
- Wilson, Samuel H
- ORCID
- Wilson, Samuel H
- Venue
- Structure
- Publisher
- Elsevier BV
- Published
- 2001-09
- Volume
- 9
- Issue
- 9
- Pages
- 759-764
- ISSN
- 0969-2126 (ISSN-L)
- OpenAlex
- W2072434779
- Cited by
- 25
- References
- 44
- Citations by year
- 2017: 1 · 2014: 1 · 2013: 1 · 2012: 1
- FWCI
- 0.78
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Structure (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- DNA damage bypass, DNA polymerase eta, DinB, archaeal DNA polymerase, polymerase structure, thymine-thymine dimers, catalytic fragment
- MeSH terms
- DNA-Directed DNA Polymerase, Humans, Models, Molecular, Protein Binding, Structure-Activity Relationship, Substrate Specificity, Protein Structure, Tertiary, Archaeal Proteins
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