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- PDB-9d3x: Crystal structure of S. thermophilus class III ribonucleotide red... -

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Basic information

Entry
Database: PDB / ID: 9d3x
TitleCrystal structure of S. thermophilus class III ribonucleotide reductase bound to dATP
ComponentsAnaerobic ribonucleoside-triphosphate reductase
KeywordsOXIDOREDUCTASE / Ribonucleotide reductase / allosteric regulation / cone domain / glycyl radical enzyme
Function / homology
Function and homology information


ribonucleoside-triphosphate reductase (thioredoxin) / anaerobic ribonucleoside-triphosphate reductase complex / ribonucleoside-triphosphate reductase (thioredoxin) activity / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / DNA replication / ATP binding
Similarity search - Function
Ribonucleoside-triphosphate reductase, anaerobic / Anaerobic ribonucleoside-triphosphate reductase / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Glycine radical domain / Glycine radical domain profile. / ATP-cone domain / ATP cone domain / ATP-cone domain profile.
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Anaerobic ribonucleoside-triphosphate reductase
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAndree, G.A. / Miller, K.R. / Drennan, C.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126982 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)T32ES007020 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Sci Adv / Year: 2025
Title: How ATP and dATP reposition class III ribonucleotide reductase cone domains to regulate enzyme activity.
Authors: Gisele A Andree / Kelsey R Miller-Brown / Zhuangyu Zhao / Ally K Smith / Christopher D Dawson / Daniel J Deredge / Catherine L Drennan /
Abstract: Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides. In the majority of cases, RNR activity is allosterically regulated by the cellular 2'- ...Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides. In the majority of cases, RNR activity is allosterically regulated by the cellular 2'-deoxyadenosine 5'-triphosphate (dATP)/adenosine 5'-triphosphate (ATP) ratio. To investigate allosteric activity regulation in anaerobic or class III (glycyl radical containing) RNRs, we determine cryo-electron microscopy structures of the class III RNR from (StNrdD). We find that StNrdD's regulatory "cone" domains adopt markedly different conformations depending on whether the activator ATP or the inhibitor dATP is bound and that these different conformations alternatively position an "active site flap" toward the active site (ATP-bound) or away (dATP-bound). In contrast, the position of the glycyl radical domain is unaffected by the cone domain conformations, suggesting that StNrdD activity is regulated through control of substrate binding rather than control of radical transfer. Hydrogen-deuterium exchange mass spectrometry and mutagenesis support the structural findings. In addition, our structural data provide insight into the molecular basis by which ATP and dATP binding lead to the observed differential cone domain conformations.
History
DepositionAug 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2025Group: 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: Anaerobic ribonucleoside-triphosphate reductase
B: Anaerobic ribonucleoside-triphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,74329
Polymers167,1272
Non-polymers4,61627
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17420 Å2
ΔGint-284 kcal/mol
Surface area49830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.580, 97.885, 189.202
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Anaerobic ribonucleoside-triphosphate reductase


Mass: 83563.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: DF198_09700, DQL92_10155 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A3G6JS83, ribonucleoside-triphosphate reductase (thioredoxin)

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Non-polymers , 5 types, 183 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystals were grown at room temperature in 1.5 M ammonium sulfate, 0.1 M HEPES pH 7.0. Crystals were cryo-protected and nucleotides were introduced by looping through a solution of 15 % ...Details: Crystals were grown at room temperature in 1.5 M ammonium sulfate, 0.1 M HEPES pH 7.0. Crystals were cryo-protected and nucleotides were introduced by looping through a solution of 15 % glycerol, 1.5 M ammonium sulfate, 100 mM ammonium formate, 30 mM magnesium sulfate, 1 mM TCEP, 50 mM HEPES, 10 mM CTP, 10 mM dATP and plunged directly in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→48.94 Å / Num. obs: 52393 / % possible obs: 99.83 % / Redundancy: 10.2 % / CC1/2: 0.998 / Net I/σ(I): 15.98
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 10.5 % / Num. unique obs: 8323 / CC1/2: 0.925 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48.94 Å / SU ML: 0.368 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5868
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2317 2613 4.99 %
Rwork0.1729 49770 -
obs0.1757 52383 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.18 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11170 0 261 156 11587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211680
X-RAY DIFFRACTIONf_angle_d0.47615854
X-RAY DIFFRACTIONf_chiral_restr0.03991695
X-RAY DIFFRACTIONf_plane_restr0.00392017
X-RAY DIFFRACTIONf_dihedral_angle_d12.93594435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.650.38511270.26582577X-RAY DIFFRACTION98.9
2.65-2.70.36191360.24262569X-RAY DIFFRACTION99.85
2.7-2.750.33011430.22372587X-RAY DIFFRACTION99.93
2.75-2.810.30121350.22752571X-RAY DIFFRACTION99.96
2.81-2.880.29251350.22792603X-RAY DIFFRACTION99.96
2.88-2.950.30091420.22222588X-RAY DIFFRACTION99.96
2.95-3.030.31421440.23482585X-RAY DIFFRACTION99.96
3.03-3.120.26961230.21392603X-RAY DIFFRACTION99.45
3.12-3.220.30331400.21522577X-RAY DIFFRACTION99.89
3.22-3.340.26721380.20272604X-RAY DIFFRACTION99.96
3.34-3.470.25231320.19282601X-RAY DIFFRACTION100
3.47-3.630.23611460.182633X-RAY DIFFRACTION100
3.63-3.820.21911350.15912596X-RAY DIFFRACTION99.89
3.82-4.060.22411370.14852627X-RAY DIFFRACTION99.78
4.06-4.370.17931390.13722632X-RAY DIFFRACTION99.93
4.37-4.810.17251380.12422644X-RAY DIFFRACTION99.96
4.81-5.510.171410.14342656X-RAY DIFFRACTION100
5.51-6.930.19821380.1672698X-RAY DIFFRACTION99.82
6.93-48.940.19751440.14492819X-RAY DIFFRACTION99.7

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