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- PDB-7p37: Streptomyces coelicolor ATP-loaded NrdR -

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Basic information

Entry
Database: PDB / ID: 7p37
TitleStreptomyces coelicolor ATP-loaded NrdR
ComponentsTranscriptional repressor NrdR
KeywordsDNA BINDING PROTEIN / Repressor / Dodecamer / ATP-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 / ATP-cone domain / ATP cone domain / ATP-cone domain profile.
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Transcriptional repressor NrdR
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional repressor NrdR
E: Transcriptional repressor NrdR
I: Transcriptional repressor NrdR
C: Transcriptional repressor NrdR
G: Transcriptional repressor NrdR
K: Transcriptional repressor NrdR
B: Transcriptional repressor NrdR
F: Transcriptional repressor NrdR
J: Transcriptional repressor NrdR
D: Transcriptional repressor NrdR
H: Transcriptional repressor NrdR
L: Transcriptional repressor NrdR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,21748
Polymers255,26012
Non-polymers12,95736
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Also Gas-phase electrophoretic mobility molecular analysis (GEMMA).
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area54050 Å2
ΔGint-184 kcal/mol
Surface area77730 Å2

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Components

#1: Protein
Transcriptional repressor NrdR


Mass: 21271.629 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O69980
#2: Chemical...
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
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

ComponentName: Homododecameric assembly of ATP-loaded NrdR. / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.247 MDa / Experimental value: YES
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 0.4 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 FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 6317

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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: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 922502 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

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