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- PDB-9fzf: Transcriptional repressor NrdR from E. coli, ADP/dATP bound state -

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Basic information

Entry
Database: PDB / ID: 9fzf
TitleTranscriptional repressor NrdR from E. coli, ADP/dATP bound state
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'-DIPHOSPHATE / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Transcriptional repressor NrdR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.444 Å
AuthorsBimai, O. / Rozman Grinberg, I. / Sjoberg, B.M. / Logan, D.T.
Funding support Sweden, United States, 6items
OrganizationGrant numberCountry
Carl Trygger FoundationCTS 20:361 Sweden
Cancerfonden201210PJF Sweden
Wenner-Gren Foundation United States
Swedish Research Council2016-04855 Sweden
Swedish Research Council2019-03681 Sweden
Swedish Research Council2023-05074 Sweden
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
DepositionJul 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,55510
Polymers37,5392
Non-polymers2,0168
Water2,900161
1
A: Transcriptional repressor NrdR
hetero molecules

A: Transcriptional repressor NrdR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,55510
Polymers37,5392
Non-polymers2,0168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/31
Buried area5550 Å2
ΔGint-40 kcal/mol
Surface area17160 Å2
2
B: Transcriptional repressor NrdR
hetero molecules

B: Transcriptional repressor NrdR
hetero molecules

B: Transcriptional repressor NrdR
hetero molecules

B: Transcriptional repressor NrdR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,11120
Polymers75,0794
Non-polymers4,03216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area16610 Å2
ΔGint-105 kcal/mol
Surface area28170 Å2
Unit cell
Length a, b, c (Å)147.126, 147.126, 85.805
Angle α, β, γ (deg.)90, 90, 120
Int Tables number180
Space group name H-MP6222

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transcriptional repressor NrdR


Mass: 18769.650 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 169 molecules

#2: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.57 Å3/Da / Density % sol: 65.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 0.2 M ammonium acetate, 45% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.444→127.42 Å / Num. obs: 10132 / % possible obs: 95.1 % / Redundancy: 39.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.31 / Rpim(I) all: 0.05 / Rrim(I) all: 0.315 / Net I/σ(I): 10.6
Reflection shellResolution: 2.444→2.699 Å / Redundancy: 41.2 % / Rmerge(I) obs: 2.635 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 517 / CC1/2: 0.912 / Rpim(I) all: 0.413 / Rrim(I) all: 2.667 / % possible all: 84.7

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROC15-Mar-2019data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.444→127.42 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.795 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.458
RfactorNum. reflection% reflectionSelection details
Rfree0.2831 494 -RANDOM
Rwork0.2149 ---
obs0.2181 10312 49.6 %-
Displacement parametersBiso mean: 47.34 Å2
Baniso -1Baniso -2Baniso -3
1-3.3756 Å20 Å20 Å2
2--3.3756 Å20 Å2
3----6.7511 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.444→127.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 118 161 2683
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0072558HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.853452HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d980SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes442HARMONIC5
X-RAY DIFFRACTIONt_it2558HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion322SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2106SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion18.14
LS refinement shellResolution: 2.444→2.67 Å
RfactorNum. reflection% reflection
Rfree0.3244 11 -
Rwork0.2723 --
obs--9.1 %
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)
11.75210.47560.81934.6154.02346.38230.05480.19160.32580.1916-0.09440.44740.32580.44740.0396-0.03640.26930.1086-0.0705-0.0155-0.389794.2246-14.810429.8501
21.85580.2014-1.14471.715-0.3655.7767-0.0510.22820.50190.22820.0156-0.38170.5019-0.38170.03540.1485-0.04430.0044-0.2552-0.0554-0.189470.1451-8.95326.4595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 149
2X-RAY DIFFRACTION1{ A|* }A200 - 203
3X-RAY DIFFRACTION2{ B|* }B1 - 149
4X-RAY DIFFRACTION2{ B|* }B200 - 203

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