PXD047943 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Activity modulation in anaerobicribonucleotide reductases: nucleotidebinding: HDX-MS data |
Description | A small, nucleotide-binding domain, the ATP-cone, is found at the N-terminus of mostribonucleotide reductase (RNR) catalytic subunits. By binding ATP or dATP it regulates theenzyme activity of all classes of RNR. Functional and structural work on aerobic RNRs hasrevealed a plethora of ways in which dATP inhibits activity by inducing oligomerization andpreventing a productive radical transfer from one subunit to the active site in the other.Anaerobic RNRs, on the other hand, store a stable glycyl radical next to the active site and thebasis for their dATP-dependent inhibition is completely unknown. We present biochemical,biophysical and structural information on the effects of ATP and dATP binding to theanaerobic RNR from Prevotella copri . The enzyme exists in a dimer-tetramer equilibriumbiased towards dimers when two ATP molecules are bound and tetramers when two dATPmolecules are bound. In the presence of ATP, P. copri NrdD is active and has a fully orderedglycyl radical domain (GRD) in one monomer of the dimer. Binding of dATP to the ATP-coneresults in loss of activity and disordering of the GRD. The glycyl radical is formed even in thedATP-bound form, but the substrate does not bind, suggesting that dATP inhibition inanaerobic RNRs acts by disordering of the GRD more than 30 Å away from the dATP molecule,thereby preventing both substrate binding and radical mobilisation. The structures implicatea complex network of activity regulation involving the GRD, the allosteric substratespecificity site and a conserved but previously unseen flap over the active site. |
HostingRepository | PRIDE |
AnnounceDate | 2024-10-22 |
AnnouncementXML | Submission_2024-10-22_06:54:13.921.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Simon Ekström |
SpeciesList | scientific name: Prevotella corporis DSM 18810 = JCM 8529; NCBI TaxID: 1122981; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive Plus |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-12-19 05:29:47 | ID requested | |
1 | 2024-08-10 12:05:28 | announced | |
⏵ 2 | 2024-10-22 06:54:14 | announced | 2024-10-22: Updated project metadata. |
Publication List
Bimai O, Banerjee I, Rozman Grinberg I, Huang P, Hultgren L, Ekstr, ö, m S, Lundin D, Sj, ö, berg BM, Logan DT, Nucleotide binding to the ATP-cone in anaerobic ribonucleotide reductases allosterically regulates activity by modulating substrate binding. Elife, 12():(2024) [pubmed] |
10.7554/elife.89292; |
Keyword List
submitter keyword: anaerobicribonucleotide reductases, HDX-MS |
Contact List
Derek Logan |
contact affiliation | Departmentof Biochemistry & Structural Biology Lund University, Sweden |
contact email | derek.logan@biochemistry.lu.se |
lab head | |
Simon Ekström |
contact affiliation | BioMS - Swedish National Infrastructure for Biological Mass Spectrometry, Lund University, BMC D1330, 221 84 Lund, Sweden |
contact email | simon.ekstrom@med.lu.se |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD047943
- Label: PRIDE project
- Name: Activity modulation in anaerobicribonucleotide reductases: nucleotidebinding: HDX-MS data