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

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Basic information

Entry
Database: PDB / ID: 9fxk
TitleTranscription repressor NrdR from E. coli, AMPPNP/ATP-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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Transcriptional repressor NrdR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.331 Å
AuthorsBimai, O. / Logan, D.T.
Funding support Sweden, United States, 8items
OrganizationGrant numberCountry
Carl Trygger FoundationCTS 20:361 Sweden
Swedish Research Council2019-01400 Sweden
Swedish Research Council2016-04855 Sweden
Swedish Research Council2023-05074 Sweden
Swedish Research Council2022-03681 Sweden
Cancerfonden20 1210 PjF Sweden
Cancerfonden20 1287 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
DepositionJul 1, 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
E: Transcriptional repressor NrdR
F: Transcriptional repressor NrdR
G: Transcriptional repressor NrdR
H: Transcriptional repressor NrdR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,38340
Polymers144,6878
Non-polymers8,69732
Water3,369187
1
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)76,69220
Polymers72,3434
Non-polymers4,34816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15990 Å2
ΔGint-93 kcal/mol
Surface area29900 Å2
MethodPISA
2
E: Transcriptional repressor NrdR
F: Transcriptional repressor NrdR
G: Transcriptional repressor NrdR
H: Transcriptional repressor NrdR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,69220
Polymers72,3434
Non-polymers4,34816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15560 Å2
ΔGint-90 kcal/mol
Surface area30660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.797, 129.791, 143.877
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Transcriptional repressor NrdR


Mass: 18085.830 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: MHCPFCFAVDTKVIDSRLVGEGSSVRRRRQCLVCNERFTTFEVAELVMPRVVKSNDVREPFNEEKLRSGMLRALEKRPVSSDDVEMAINHIKSQLRATGEREVPSKMIGNLVMEQLKKLDKVAYIRFASVYRSFEDIKEFGEEIARLEDHHHHHH
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, 219 molecules

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


Mass: 491.182 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein at 8 mg/ml in 1.5 mM ADP, 1.1 mM AMPPNP, 25 mM Tris-HCl pH 9 (at 277 K), 300 mM NaCl, 1 mM TCEP, 10 mM MgCl2. 150 nL protein were mixed with with 50 nL reservoir solution containing ...Details: Protein at 8 mg/ml in 1.5 mM ADP, 1.1 mM AMPPNP, 25 mM Tris-HCl pH 9 (at 277 K), 300 mM NaCl, 1 mM TCEP, 10 mM MgCl2. 150 nL protein were mixed with with 50 nL reservoir solution containing 0.1 M Bis-Tris propane pH 7.5, 0.2 M potassium thiocyanate, 20% (w/v) PEG3350 at 293 K. Crystals were harvested in paraffin oil.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97963 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97963 Å / Relative weight: 1
ReflectionResolution: 2.331→96.372 Å / Num. obs: 51826 / % possible obs: 75.7 % / Redundancy: 13.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.057 / Rrim(I) all: 0.212 / Net I/σ(I): 10
Reflection shellResolution: 2.331→2.569 Å / Redundancy: 13.6 % / Rmerge(I) obs: 2.451 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2591 / CC1/2: 0.427 / Rpim(I) all: 0.687 / Rrim(I) all: 2.547 / % possible all: 15.1

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.331→96.37 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.57 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.577 / SU Rfree Blow DPI: 0.289 / SU Rfree Cruickshank DPI: 0.291
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 2573 -RANDOM
Rwork0.2243 ---
obs0.2259 51826 75.7 %-
Displacement parametersBiso mean: 64.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.0244 Å20 Å20 Å2
2--0.673 Å20 Å2
3----0.6486 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.331→96.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9669 0 504 187 10360
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00710328HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8613951HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3959SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1780HARMONIC5
X-RAY DIFFRACTIONt_it10328HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1296SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8284SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion18.65
LS refinement shellResolution: 2.331→2.48 Å
RfactorNum. reflection% reflection
Rfree0.424 58 -
Rwork0.3317 --
obs--8.97 %
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)
13.7778-2.37661.12151.2438-0.77230.51260.04210.04280.00820.0428-0.08740.04370.00820.04370.0454-0.0295-0.0325-0.022-0.0114-0.06240.0339-73.531-19.60542.0195
21.68761.28570.10633.1710.80650.8350.0266-0.164-0.0337-0.164-0.01860.0286-0.03370.0286-0.008-0.0720.01110.02510.02420.0565-0.038-86.610114.410839.1343
33.1579-2.8006-0.59952.02510.862800.08190.0029-0.08310.0029-0.0006-0.0682-0.0831-0.0682-0.0813-0.00330.00720.08190.05620.10710.0058-58.1613.404336.0638
41.26671.4183-1.37362.0537-1.30671.7248-0.0712-0.0050.0314-0.0050.1232-0.19880.0314-0.1988-0.052-0.0585-0.0136-0.02940.0545-0.0049-0.081-44.8934-19.644743.5739
54.25193.972-0.88284.755-1.1550.71560.08930.0475-0.0250.0475-0.05580.0387-0.0250.0387-0.0335-0.01880.05020.0438-0.0932-0.0945-0.1482-27.649914.38492.1681
61.4737-0.9427-0.8653.95422.42023.58780.06190.19760.23220.1976-0.142-0.17820.2322-0.17820.0801-0.069-0.0613-0.0648-0.08870.0817-0.1428-37.9005-19.4989-4.6382
73.59573.16141.14964.04020.54681.49040.07570.2676-0.15630.2676-0.1402-0.062-0.1563-0.0620.0645-0.16950.1158-0.0131-0.13380.1835-0.0332-9.5226-18.095-1.9328
82.5739-0.3954-0.5653.46020.17531.02530.08820.43980.1020.4398-0.08590.03890.1020.0389-0.00220.0137-0.0806-0.06410.01980.0224-0.2151-0.157916.8631-0.4637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 150
2X-RAY DIFFRACTION1{ A|* }A200 - 203
3X-RAY DIFFRACTION2{ B|* }B1 - 150
4X-RAY DIFFRACTION2{ B|* }B200 - 203
5X-RAY DIFFRACTION3{ C|* }C1 - 150
6X-RAY DIFFRACTION3{ C|* }C200 - 203
7X-RAY DIFFRACTION4{ D|* }D1 - 150
8X-RAY DIFFRACTION4{ D|* }D200 - 203
9X-RAY DIFFRACTION5{ E|* }E1 - 150
10X-RAY DIFFRACTION5{ E|* }E200 - 203
11X-RAY DIFFRACTION6{ F|* }F1 - 149
12X-RAY DIFFRACTION6{ F|* }F200 - 203
13X-RAY DIFFRACTION7{ G|* }G1 - 151
14X-RAY DIFFRACTION7{ G|* }G200 - 203
15X-RAY DIFFRACTION8{ H|* }H1 - 149
16X-RAY DIFFRACTION8{ H|* }H200 - 203

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