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- PDB-7p3f: Streptomyces coelicolor dATP/ATP-loaded NrdR in complex with its ... -

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Basic information

Entry
Database: PDB / ID: 7p3f
TitleStreptomyces coelicolor dATP/ATP-loaded NrdR in complex with its cognate DNA
Components
  • (DNA (50-MER)) x 2
  • Transcriptional repressor NrdR
KeywordsDNA BINDING PROTEIN / Repressor / Dodecamer / ATP-binding / dATP-binding
Function / homology
Function and homology information


negative regulation of DNA-templated transcription / DNA binding / zinc ion binding / ATP binding
Similarity search - Function
Ribonucleotide reductase regulator NrdR-like / Transcriptional repressor NrdR-like, N-terminal domain / ATP-cone domain / ATP cone domain / ATP-cone domain profile.
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / Transcriptional repressor NrdR
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
Streptomyces coelicolor A3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsMartinez-Carranza, M. / Stenmark, P.
Funding support Sweden, 5items
OrganizationGrant numberCountry
Swedish Research Council2018-03406 Sweden
Swedish Research Council2019-01400 Sweden
Wenner-Gren Foundation Sweden
Cancerfonden20 1287 PjF Sweden
Cancerfonden2018/820 Sweden
CitationJournal: Nat Commun / Year: 2022
Title: A nucleotide-sensing oligomerization mechanism that controls NrdR-dependent transcription of ribonucleotide reductases.
Authors: Inna Rozman Grinberg / Markel Martínez-Carranza / Ornella Bimai / Ghada Nouaïria / Saher Shahid / Daniel Lundin / Derek T Logan / Britt-Marie Sjöberg / Pål Stenmark /
Abstract: 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 ...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.
History
DepositionJul 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional repressor NrdR
C: Transcriptional repressor NrdR
B: Transcriptional repressor NrdR
D: Transcriptional repressor NrdR
F: DNA (50-MER)
R: DNA (50-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,47618
Polymers120,2216
Non-polymers4,25512
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, The complex was observed in microscale thermophoresis (MST) and gas-phase electrophoretic mobility molecular analysis (GEMMA).
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area25020 Å2
ΔGint-96 kcal/mol
Surface area42280 Å2
MethodPISA

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Components

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Protein , 1 types, 4 molecules ACBD

#1: Protein
Transcriptional repressor NrdR


Mass: 21271.629 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: nrdR, SCO5804, SC4H2.25 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O69980

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DNA chain , 2 types, 2 molecules FR

#2: DNA chain DNA (50-MER)


Mass: 17507.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces coelicolor A3(2) (bacteria)
#3: DNA chain DNA (50-MER)


Mass: 17627.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces coelicolor A3(2) (bacteria)

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Non-polymers , 3 types, 12 molecules

#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Tetrameric assembly of dATP/ATP-loaded NrdR in complex with its cognate DNACOMPLEX#1-#30RECOMBINANT
2Transcriptional repressor NrdRCOMPLEX#11RECOMBINANT
3DNA (50-MER)COMPLEX#2-#31RECOMBINANT
Molecular weightValue: 0.125 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Streptomyces coelicolor A3(2) (bacteria)100226
33Streptomyces coelicolor A3(2) (bacteria)100226
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli BL21(DE3) (bacteria)469008
33Synthetic construct (others)32630
Buffer solutionpH: 8
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3562

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4cryoSPARC3.1CTF correction
7PHENIX1.19.2model fitting
8Coot0.9.5model fitting
10cryoSPARC3.1initial Euler assignment
11cryoSPARC3.1final Euler assignment
12cryoSPARC3.1classification
13cryoSPARC3.13D reconstruction
14PHENIX1.19.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 445937 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7P37

7p37


Pdb chain-ID: A / Accession code: 7P37 / Pdb chain residue range: 1-147 / Source name: PDB / Type: experimental model

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