An endogenous dAMP ligand in
© 2018 National Academy of Sciences. All rights reserved. The high fidelity of DNA replication and repair is attributable, in part, to the allosteric regulation of ribonucleotide reductases (RNRs) that maintains proper deoxynucleotide pool sizes and ratios in vivo. In class Ia RNRs, ATP (stimulatory...
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Proceedings of the National Academy of Sciences
2018
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| Online Access: | http://hdl.handle.net/1721.1/118869 https://orcid.org/0000-0001-7174-0485 https://orcid.org/0000-0001-8076-4489 |
| _version_ | 1811097294446002176 |
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| author | Maggiolo, Ailiena O. Thomas, William C. Meisburger, Steve P. Boal, Amie K. Parker, Mackenzie James Kim, Albert Dong Woo Ando, Nozomi Stubbe, JoAnne |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Maggiolo, Ailiena O. Thomas, William C. Meisburger, Steve P. Boal, Amie K. Parker, Mackenzie James Kim, Albert Dong Woo Ando, Nozomi Stubbe, JoAnne |
| author_sort | Maggiolo, Ailiena O. |
| collection | MIT |
| description | © 2018 National Academy of Sciences. All rights reserved. The high fidelity of DNA replication and repair is attributable, in part, to the allosteric regulation of ribonucleotide reductases (RNRs) that maintains proper deoxynucleotide pool sizes and ratios in vivo. In class Ia RNRs, ATP (stimulatory) and dATP (inhibitory) regulate activity by binding to the ATP-cone domain at the N terminus of the large α subunit and altering the enzyme’s quaternary structure. Class Ib RNRs, in contrast, have a partial cone domain and have generally been found to be insensitive to dATP inhibition. An exception is the Bacillus subtilis Ib RNR, which we recently reported to be inhibited by physiological concentrations of dATP. Here, we demonstrate that the α subunit of this RNR contains tightly bound deoxyadenosine 5′-monophosphate (dAMP) in its N-terminal domain and that dATP inhibition of CDP reduction is enhanced by its presence. X-ray crystallography reveals a previously unobserved (noncanonical) α2dimer with its entire interface composed of the partial N-terminal cone domains, each binding a dAMP molecule. Using small-angle X-ray scattering (SAXS), we show that this noncanonical α2dimer is the predominant form of the dAMP-bound α in solution and further show that addition of dATP leads to the formation of larger oligomers. Based on this information, we propose a model to describe the mechanism by which the noncanonical α2inhibits the activity of the B. subtilis Ib RNR in a dATP- and dAMP-dependent manner. |
| first_indexed | 2024-09-23T16:57:21Z |
| format | Article |
| id | mit-1721.1/118869 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T16:57:21Z |
| publishDate | 2018 |
| publisher | Proceedings of the National Academy of Sciences |
| record_format | dspace |
| spelling | mit-1721.1/1188692022-09-29T22:39:34Z An endogenous dAMP ligand in Maggiolo, Ailiena O. Thomas, William C. Meisburger, Steve P. Boal, Amie K. Parker, Mackenzie James Kim, Albert Dong Woo Ando, Nozomi Stubbe, JoAnne Massachusetts Institute of Technology. Department of Biology Massachusetts Institute of Technology. Department of Chemistry Massachusetts Institute of Technology. Department of Physics Parker, Mackenzie James Kim, Albert Dong Woo Ando, Nozomi Stubbe, JoAnne © 2018 National Academy of Sciences. All rights reserved. The high fidelity of DNA replication and repair is attributable, in part, to the allosteric regulation of ribonucleotide reductases (RNRs) that maintains proper deoxynucleotide pool sizes and ratios in vivo. In class Ia RNRs, ATP (stimulatory) and dATP (inhibitory) regulate activity by binding to the ATP-cone domain at the N terminus of the large α subunit and altering the enzyme’s quaternary structure. Class Ib RNRs, in contrast, have a partial cone domain and have generally been found to be insensitive to dATP inhibition. An exception is the Bacillus subtilis Ib RNR, which we recently reported to be inhibited by physiological concentrations of dATP. Here, we demonstrate that the α subunit of this RNR contains tightly bound deoxyadenosine 5′-monophosphate (dAMP) in its N-terminal domain and that dATP inhibition of CDP reduction is enhanced by its presence. X-ray crystallography reveals a previously unobserved (noncanonical) α2dimer with its entire interface composed of the partial N-terminal cone domains, each binding a dAMP molecule. Using small-angle X-ray scattering (SAXS), we show that this noncanonical α2dimer is the predominant form of the dAMP-bound α in solution and further show that addition of dATP leads to the formation of larger oligomers. Based on this information, we propose a model to describe the mechanism by which the noncanonical α2inhibits the activity of the B. subtilis Ib RNR in a dATP- and dAMP-dependent manner. National Science Foundation (U.S.) (grant NSF-0070319) United States. Department of Energy. Office of Science (contract DE-AC02-06CH11357) National Cancer Institute (U.S.) (Grant ACB-12002) National Institute of General Medical Sciences (U.S.) (Grant AGM-12006) National Institutes of Health (U.S.). Office of Research Infrastructure Programs (High-End Instrumentation Grant 1S10OD01 2289-01A1) Michigan Economic Development Corporation Michigan Technology Tri-Corridor (Grant 085P1000817) United States. Department of Energy. Office of Science User Facility (Contract DE-AC02-05CH11231) National Science Foundation (U.S.) (grant DMR-1332208) National Institute of General Medical Sciences (U.S.) (Grant GM-10348) National Institutes of Health (U.S.) (grant GM10008) National Institutes of Health (U.S.) (grant GM1247) National Institutes of Health (U.S.) (grant GM081393) Princeton University (start-up funds) 2018-11-05T14:20:09Z 2018-11-05T14:20:09Z 2018-04 2018-10-12T16:24:50Z Article http://purl.org/eprint/type/JournalArticle 0027-8424 1091-6490 http://hdl.handle.net/1721.1/118869 Parker, Mackenzie J., Ailiena O. Maggiolo, William C. Thomas, Albert Kim, Steve P. Meisburger, Nozomi Ando, Amie K. Boal, and JoAnne Stubbe. “An Endogenous dAMP Ligand inBacillus Subtilisclass Ib RNR Promotes Assembly of a Noncanonical Dimer for Regulation by dATP.” Proceedings of the National Academy of Sciences 115, no. 20 (April 30, 2018): E4594–E4603. https://orcid.org/0000-0001-7174-0485 https://orcid.org/0000-0001-8076-4489 http://dx.doi.org/10.1073/PNAS.1800356115 Proceedings of the National Academy of Sciences Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf Proceedings of the National Academy of Sciences PNAS |
| spellingShingle | Maggiolo, Ailiena O. Thomas, William C. Meisburger, Steve P. Boal, Amie K. Parker, Mackenzie James Kim, Albert Dong Woo Ando, Nozomi Stubbe, JoAnne An endogenous dAMP ligand in |
| title | An endogenous dAMP ligand in |
| title_full | An endogenous dAMP ligand in |
| title_fullStr | An endogenous dAMP ligand in |
| title_full_unstemmed | An endogenous dAMP ligand in |
| title_short | An endogenous dAMP ligand in |
| title_sort | endogenous damp ligand in |
| url | http://hdl.handle.net/1721.1/118869 https://orcid.org/0000-0001-7174-0485 https://orcid.org/0000-0001-8076-4489 |
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