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PXD047943-1

PXD047943 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleActivity modulation in anaerobicribonucleotide reductases: nucleotidebinding: HDX-MS data
DescriptionA 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.
HostingRepositoryPRIDE
AnnounceDate2024-08-10
AnnouncementXMLSubmission_2024-08-10_12:05:27.115.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterSimon Ekström
SpeciesList scientific name: Prevotella corporis DSM 18810 = JCM 8529; NCBI TaxID: 1122981;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive Plus
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-12-19 05:29:47ID requested
12024-08-10 12:05:28announced
22024-10-22 06:54:14announced2024-10-22: 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 affiliationDepartmentof Biochemistry & Structural Biology Lund University, Sweden
contact emailderek.logan@biochemistry.lu.se
lab head
Simon Ekström
contact affiliationBioMS - Swedish National Infrastructure for Biological Mass Spectrometry, Lund University, BMC D1330, 221 84 Lund, Sweden
contact emailsimon.ekstrom@med.lu.se
dataset submitter
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Dataset FTP location
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