The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.
Saved in:
| Title: | The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions. |
|---|---|
| Authors: | Mullins, Elwood A., Shi, Rongxin, Parsons, Zachary D., Yuen, Philip K., David, Sheila S., Igarashi, Yasuhiro, Eichman, Brandt F. |
| Source: | Nature. 11/12/2015, Vol. 527 Issue 7577, p254-258. 5p. 7 Diagrams, 3 Charts, 3 Graphs. |
| Subjects: | DNA glycosylases, DNA ligases, Nucleotides, DNA adducts, DNA repair |
| Abstract: | Threats to genomic integrity arising from DNA damage are mitigated by DNA glycosylases, which initiate the base excision repair pathway by locating and excising aberrant nucleobases. How these enzymes find small modifications within the genome is a current area of intensive research. A hallmark of these and other DNA repair enzymes is their use of base flipping to sequester modified nucleotides from the DNA helix and into an active site pocket. Consequently, base flipping is generally regarded as an essential aspect of lesion recognition and a necessary precursor to base excision. Here we present the first, to our knowledge, DNA glycosylase mechanism that does not require base flipping for either binding or catalysis. Using the DNA glycosylase AlkD from Bacillus cereus, we crystallographically monitored excision of an alkylpurine substrate as a function of time, and reconstructed the steps along the reaction coordinate through structures representing substrate, intermediate and product complexes. Instead of directly interacting with the damaged nucleobase, AlkD recognizes aberrant base pairs through interactions with the phosphoribose backbone, while the lesion remains stacked in the DNA duplex. Quantum mechanical calculations revealed that these contacts include catalytic charge-dipole and CH-π interactions that preferentially stabilize the transition state. We show in vitro and in vivo how this unique means of recognition and catalysis enables AlkD to repair large adducts formed by yatakemycin, a member of the duocarmycin family of antimicrobial natural products exploited in bacterial warfare and chemotherapeutic trials. Bulky adducts of this or any type are not excised by DNA glycosylases that use a traditional base-flipping mechanism. Hence, these findings represent a new model for DNA repair and provide insights into catalysis of base excision. [ABSTRACT FROM AUTHOR] |
| Copyright of Nature is the property of Springer Nature and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Psychology and Behavioral Sciences Collection |
| FullText | Links: – Type: pdflink Text: Availability: 0 |
|---|---|
| Header | DbId: pbh DbLabel: Psychology and Behavioral Sciences Collection An: 111020982 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
| IllustrationInfo | |
| Items | – Name: Title Label: Title Group: Ti Data: The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Mullins%2C+Elwood+A%2E%22">Mullins, Elwood A.</searchLink><br /><searchLink fieldCode="AR" term="%22Shi%2C+Rongxin%22">Shi, Rongxin</searchLink><br /><searchLink fieldCode="AR" term="%22Parsons%2C+Zachary+D%2E%22">Parsons, Zachary D.</searchLink><br /><searchLink fieldCode="AR" term="%22Yuen%2C+Philip+K%2E%22">Yuen, Philip K.</searchLink><br /><searchLink fieldCode="AR" term="%22David%2C+Sheila+S%2E%22">David, Sheila S.</searchLink><br /><searchLink fieldCode="AR" term="%22Igarashi%2C+Yasuhiro%22">Igarashi, Yasuhiro</searchLink><br /><searchLink fieldCode="AR" term="%22Eichman%2C+Brandt+F%2E%22">Eichman, Brandt F.</searchLink> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Nature%22">Nature</searchLink>. 11/12/2015, Vol. 527 Issue 7577, p254-258. 5p. 7 Diagrams, 3 Charts, 3 Graphs. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22DNA+glycosylases%22">DNA glycosylases</searchLink><br /><searchLink fieldCode="DE" term="%22DNA+ligases%22">DNA ligases</searchLink><br /><searchLink fieldCode="DE" term="%22Nucleotides%22">Nucleotides</searchLink><br /><searchLink fieldCode="DE" term="%22DNA+adducts%22">DNA adducts</searchLink><br /><searchLink fieldCode="DE" term="%22DNA+repair%22">DNA repair</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Threats to genomic integrity arising from DNA damage are mitigated by DNA glycosylases, which initiate the base excision repair pathway by locating and excising aberrant nucleobases. How these enzymes find small modifications within the genome is a current area of intensive research. A hallmark of these and other DNA repair enzymes is their use of base flipping to sequester modified nucleotides from the DNA helix and into an active site pocket. Consequently, base flipping is generally regarded as an essential aspect of lesion recognition and a necessary precursor to base excision. Here we present the first, to our knowledge, DNA glycosylase mechanism that does not require base flipping for either binding or catalysis. Using the DNA glycosylase AlkD from Bacillus cereus, we crystallographically monitored excision of an alkylpurine substrate as a function of time, and reconstructed the steps along the reaction coordinate through structures representing substrate, intermediate and product complexes. Instead of directly interacting with the damaged nucleobase, AlkD recognizes aberrant base pairs through interactions with the phosphoribose backbone, while the lesion remains stacked in the DNA duplex. Quantum mechanical calculations revealed that these contacts include catalytic charge-dipole and CH-π interactions that preferentially stabilize the transition state. We show in vitro and in vivo how this unique means of recognition and catalysis enables AlkD to repair large adducts formed by yatakemycin, a member of the duocarmycin family of antimicrobial natural products exploited in bacterial warfare and chemotherapeutic trials. Bulky adducts of this or any type are not excised by DNA glycosylases that use a traditional base-flipping mechanism. Hence, these findings represent a new model for DNA repair and provide insights into catalysis of base excision. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Nature is the property of Springer Nature and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
| PLink | https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=pbh&AN=111020982 |
| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1038/nature15728 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 5 StartPage: 254 Subjects: – SubjectFull: DNA glycosylases Type: general – SubjectFull: DNA ligases Type: general – SubjectFull: Nucleotides Type: general – SubjectFull: DNA adducts Type: general – SubjectFull: DNA repair Type: general Titles: – TitleFull: The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Mullins, Elwood A. – PersonEntity: Name: NameFull: Shi, Rongxin – PersonEntity: Name: NameFull: Parsons, Zachary D. – PersonEntity: Name: NameFull: Yuen, Philip K. – PersonEntity: Name: NameFull: David, Sheila S. – PersonEntity: Name: NameFull: Igarashi, Yasuhiro – PersonEntity: Name: NameFull: Eichman, Brandt F. IsPartOfRelationships: – BibEntity: Dates: – D: 12 M: 11 Text: 11/12/2015 Type: published Y: 2015 Identifiers: – Type: issn-print Value: 00280836 Numbering: – Type: volume Value: 527 – Type: issue Value: 7577 Titles: – TitleFull: Nature Type: main |
| ResultId | 1 |
