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TitleA nucleotide-sensing oligomerization mechanism that controls NrdR-dependent transcription of ribonucleotide reductases.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 2700, Year 2022
Publish dateMay 16, 2022
AuthorsInna Rozman Grinberg / Markel Martínez-Carranza / Ornella Bimai / Ghada Nouaïria / Saher Shahid / Daniel Lundin / Derek T Logan / Britt-Marie Sjöberg / Pål Stenmark /
PubMed AbstractRibonucleotide reductase (RNR) is an essential enzyme that catalyzes the synthesis of DNA building blocks in virtually all living cells. NrdR, an RNR-specific repressor, controls the transcription of ...Ribonucleotide reductase (RNR) is an essential enzyme that catalyzes the synthesis of DNA building blocks in virtually all living cells. NrdR, an RNR-specific repressor, controls the transcription of RNR genes and, often, its own, in most bacteria and some archaea. NrdR senses the concentration of nucleotides through its ATP-cone, an evolutionarily mobile domain that also regulates the enzymatic activity of many RNRs, while a Zn-ribbon domain mediates binding to NrdR boxes upstream of and overlapping the transcription start site of RNR genes. Here, we combine biochemical and cryo-EM studies of NrdR from Streptomyces coelicolor to show, at atomic resolution, how NrdR binds to DNA. The suggested mechanism involves an initial dodecamer loaded with two ATP molecules that cannot bind to DNA. When dATP concentrations increase, an octamer forms that is loaded with one molecule each of dATP and ATP per monomer. A tetramer derived from this octamer then binds to DNA and represses transcription of RNR. In many bacteria - including well-known pathogens such as Mycobacterium tuberculosis - NrdR simultaneously controls multiple RNRs and hence DNA synthesis, making it an excellent target for novel antibiotics development.
External linksNat Commun / PubMed:35577776 / PubMed Central
MethodsEM (single particle)
Resolution2.96 - 3.31 Å
Structure data

13178

7p37

EMDB-13178, PDB-7p37:
Streptomyces coelicolor ATP-loaded NrdR
Method: EM (single particle) / Resolution: 2.96 Å

13179

7p3f

EMDB-13179, PDB-7p3f:
Streptomyces coelicolor dATP/ATP-loaded NrdR in complex with its cognate DNA
Method: EM (single particle) / Resolution: 3.31 Å

13182

7p3q

EMDB-13182, PDB-7p3q:
Streptomyces coelicolor dATP/ATP-loaded NrdR octamer
Method: EM (single particle) / Resolution: 3.12 Å

Chemicals

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-ZN:
Unknown entry

ChemComp-DTP:
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

Source
  • streptomyces coelicolor a3(2) (bacteria)
  • streptomyces coelicolor (strain atcc baa-471 / a3(2) / m145) (bacteria)
KeywordsDNA BINDING PROTEIN / Repressor / Dodecamer / ATP-binding / dATP-binding

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