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- PDB-9fvr: Transcription repressor NrdR from E. coli, ATP/dATP-bound state, ... -

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Basic information

Entry
Database: PDB / ID: 9fvr
TitleTranscription repressor NrdR from E. coli, ATP/dATP-bound state, SeMet protein
ComponentsTranscriptional repressor NrdR
KeywordsDNA BINDING PROTEIN / Ribonucleotide reductase / transcriptional repressor / ATP-cone domain / Zn-ribbon domain
Function / homology
Function and homology information


double-stranded DNA binding / negative regulation of DNA-templated transcription / 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 / Transcriptional repressor NrdR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.099 Å
AuthorsBimai, O. / Sjoberg, B.M. / Rozman Grinberg, I. / Logan, D.T.
Funding support Sweden, United States, 6items
OrganizationGrant numberCountry
Carl Trygger FoundationCTS 20:361 Sweden
Swedish Research Council2019-01400 Sweden
Swedish Research Council2016-04855 Sweden
Swedish Research Council2023-05074 Sweden
Cancerfonden20 1210 PjF Sweden
Wenner-Gren Foundation United States
CitationJournal: FEBS J / Year: 2025
Title: Bacterial transcriptional repressor NrdR - a flexible multifactorial nucleotide sensor.
Authors: Inna Rozman Grinberg / Ornella Bimaï / Saher Shahid / Lena Philipp / Markel Martínez-Carranza / Ipsita Banerjee / Daniel Lundin / Pål Stenmark / Britt-Marie Sjöberg / Derek T Logan /
Abstract: NrdR is a bacterial transcriptional repressor consisting of a zinc (Zn)-ribbon domain followed by an ATP-cone domain. Understanding its mechanism of action could aid the design of novel ...NrdR is a bacterial transcriptional repressor consisting of a zinc (Zn)-ribbon domain followed by an ATP-cone domain. Understanding its mechanism of action could aid the design of novel antibacterials. NrdR binds specifically to two "NrdR boxes" upstream of ribonucleotide reductase operons, of which Escherichia coli has three: nrdHIEF, nrdDG and nrdAB, in the last of which we identified a new box. We show that E. coli NrdR (EcoNrdR) has similar binding strength to all three sites when loaded with ATP plus deoxyadenosine triphosphate (dATP) or equivalent diphosphate combinations. No other combination of adenine nucleotides promotes binding to DNA. We present crystal structures of EcoNrdR-ATP-dATP and EcoNrdR-ADP-dATP, which are the first high-resolution crystal structures of an NrdR. We have also determined cryo-electron microscopy structures of DNA-bound EcoNrdR-ATP-dATP and novel filaments of EcoNrdR-ATP. Tetrameric forms of EcoNrdR involve alternating interactions between pairs of Zn-ribbon domains and ATP-cones. The structures reveal considerable flexibility in relative orientation of ATP-cones vs Zn-ribbon domains. The structure of DNA-bound EcoNrdR-ATP-dATP shows that significant conformational rearrangements between ATP-cones and Zn-ribbons accompany DNA binding while the ATP-cones retain the same relative orientation. In contrast, ATP-loaded EcoNrdR filaments show rearrangements of the ATP-cone pairs and sequester the DNA-binding residues of NrdR such that they are unable to bind to DNA. Our results, in combination with a previous structural and biochemical study, point to highly flexible EcoNrdR structures that, when loaded with the correct nucleotides, adapt to an optimal promoter-binding conformation.
History
DepositionJun 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional repressor NrdR
B: Transcriptional repressor NrdR
C: Transcriptional repressor NrdR
D: Transcriptional repressor NrdR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,99521
Polymers73,4134
Non-polymers4,58217
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16320 Å2
ΔGint-194 kcal/mol
Surface area30420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.792, 73.832, 138.046
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Transcriptional repressor NrdR


Mass: 18353.178 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nrdR, ybaD, b0413, JW0403 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8D0
#2: 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
#3: 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
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.2 M MgCl2, 12.5% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.099→65.1 Å / Num. obs: 10661 / % possible obs: 92.6 % / Redundancy: 13.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.062 / Rrim(I) all: 0.224 / Net I/σ(I): 8.4
Reflection shellResolution: 3.099→3.37 Å / Redundancy: 12.3 % / Rmerge(I) obs: 2.082 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 534 / CC1/2: 0.616 / Rpim(I) all: 0.606 / Rrim(I) all: 2.17 / % possible all: 17.8

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSJan 31, 2020 BUILT=20200131data scaling
XDSJan 31, 2020 BUILT=20200131data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.099→31.85 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.904 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.63
RfactorNum. reflection% reflectionSelection details
Rfree0.2738 552 -RANDOM
Rwork0.2242 ---
obs0.227 10644 77.8 %-
Displacement parametersBiso mean: 118 Å2
Baniso -1Baniso -2Baniso -3
1--2.4029 Å20 Å20 Å2
2--4.0295 Å20 Å2
3----1.6266 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 3.099→31.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4878 0 253 1 5132
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0065209HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.837037HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1989SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes882HARMONIC5
X-RAY DIFFRACTIONt_it5209HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion651SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3930SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.06
X-RAY DIFFRACTIONt_other_torsion20.85
LS refinement shellResolution: 3.1→3.33 Å
RfactorNum. reflection% reflection
Rfree0.4172 17 -
Rwork0.2841 --
obs0.2899 395 15.32 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7501-1.1958-1.27964.99025.0197.0783-0.00990.2721-0.15860.27210.2057-0.2199-0.1586-0.2199-0.1958-0.37190.0352-0.1262-0.12540.0788-0.24718.164815.850448.982
23.9068-0.82452.06582.22-1.22163.19120.1097-0.23870.1927-0.23870.0608-0.06390.1927-0.0639-0.1705-0.2427-0.10780.072-0.1614-0.0856-0.36359.86047.69112.3807
32.85253.40813.13953.74654.62197.00750.2251-0.13110.3702-0.13110.2551-0.20690.3702-0.2069-0.4802-0.23880.0188-0.0409-0.13930.0686-0.34059.61729.936914.051
42.61470.2626-0.83912.8304-2.23366.1816-0.07180.1452-0.07090.14520.13470.0492-0.07090.0492-0.0629-0.29780.0401-0.1486-0.215-0.0449-0.220117.005238.505350.8553
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 150
2X-RAY DIFFRACTION1{ A|* }A200 - 202
3X-RAY DIFFRACTION2{ B|* }B1 - 149
4X-RAY DIFFRACTION2{ B|* }B200 - 202
5X-RAY DIFFRACTION3{ C|* }C1 - 153
6X-RAY DIFFRACTION3{ C|* }C200 - 202
7X-RAY DIFFRACTION4{ D|* }D1 - 151
8X-RAY DIFFRACTION4{ D|* }D200 - 202

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