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- PDB-3paw: Low resolution X-ray crystal structure of Yeast Rnr1p with dATP b... -

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Basic information

Entry
Database: PDB / ID: 3paw
TitleLow resolution X-ray crystal structure of Yeast Rnr1p with dATP bound in the A-site
ComponentsRibonucleoside-diphosphate reductase large chain 1
KeywordsOXIDOREDUCTASE / Ribonucleotide reductase / Nucleotide binding
Function / homology
Function and homology information


Interconversion of nucleotide di- and triphosphates / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / nucleotide binding / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain
Similarity search - Domain/homology
Ribonucleoside-diphosphate reductase large chain 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.61 Å
AuthorsFairman, J.W. / Wijerathna, S.R. / Dealwis, C.G.
CitationJournal: Nat Struct Mol Biol / Year: 2011
Title: Structural basis for allosteric regulation of human ribonucleotide reductase by nucleotide-induced oligomerization.
Authors: James Wesley Fairman / Sanath Ranjan Wijerathna / Md Faiz Ahmad / Hai Xu / Ryo Nakano / Shalini Jha / Jay Prendergast / R Martin Welin / Susanne Flodin / Annette Roos / Pär Nordlund / ...Authors: James Wesley Fairman / Sanath Ranjan Wijerathna / Md Faiz Ahmad / Hai Xu / Ryo Nakano / Shalini Jha / Jay Prendergast / R Martin Welin / Susanne Flodin / Annette Roos / Pär Nordlund / Zongli Li / Thomas Walz / Chris Godfrey Dealwis /
Abstract: Ribonucleotide reductase (RR) is an α(n)β(n) (RR1-RR2) complex that maintains balanced dNTP pools by reducing NDPs to dNDPs. RR1 is the catalytic subunit, and RR2 houses the free radical required ...Ribonucleotide reductase (RR) is an α(n)β(n) (RR1-RR2) complex that maintains balanced dNTP pools by reducing NDPs to dNDPs. RR1 is the catalytic subunit, and RR2 houses the free radical required for catalysis. RR is allosterically regulated by its activator ATP and its inhibitor dATP, which regulate RR activity by inducing oligomerization of RR1. Here, we report the first X-ray structures of human RR1 bound to TTP alone, dATP alone, TTP-GDP, TTP-ATP, and TTP-dATP. These structures provide insights into regulation of RR by ATP or dATP. At physiological dATP concentrations, RR1 forms inactive hexamers. We determined the first X-ray structure of the RR1-dATP hexamer and used single-particle electron microscopy to visualize the α(6)-ββ'-dATP holocomplex. Site-directed mutagenesis and functional assays confirm that hexamerization is a prerequisite for inhibition by dATP. Our data indicate a mechanism for regulating RR activity by dATP-induced oligomerization.
History
DepositionOct 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase large chain 1
B: Ribonucleoside-diphosphate reductase large chain 1
C: Ribonucleoside-diphosphate reductase large chain 1
D: Ribonucleoside-diphosphate reductase large chain 1


Theoretical massNumber of molelcules
Total (without water)398,6924
Polymers398,6924
Non-polymers00
Water00
1
A: Ribonucleoside-diphosphate reductase large chain 1
B: Ribonucleoside-diphosphate reductase large chain 1


Theoretical massNumber of molelcules
Total (without water)199,3462
Polymers199,3462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-12 kcal/mol
Surface area62820 Å2
MethodPISA
2
C: Ribonucleoside-diphosphate reductase large chain 1
D: Ribonucleoside-diphosphate reductase large chain 1


Theoretical massNumber of molelcules
Total (without water)199,3462
Polymers199,3462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-8 kcal/mol
Surface area63760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.509, 166.509, 381.697
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Ribonucleoside-diphosphate reductase large chain 1 / Ribonucleotide reductase R1 subunit 1 / Ribonucleotide reductase large subunit 1


Mass: 99672.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RNR1, CRT7, RIR1, SDS12, YER070W / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: P21524, ribonucleoside-diphosphate reductase

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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: 3.83 Å3/Da / Density % sol: 67.9 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 6.61→192.45 Å / Num. obs: 9893

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 6.61→192.45 Å / Cor.coef. Fo:Fc: 0.674 / Cor.coef. Fo:Fc free: 0.531 / SU B: 0.006 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 3.423 / ESU R Free: 3.869 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.44181 469 4.8 %RANDOM
Rwork0.39084 ---
obs0.39326 9378 87.75 %-
all-9893 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.172 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 6.61→192.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14596 0 0 0 14596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02224148
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.95632700
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.46552948
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92923.9071116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.559154220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.25915152
X-RAY DIFFRACTIONr_chiral_restr0.0920.23584
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02118264
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2451.514716
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.445223800
X-RAY DIFFRACTIONr_scbond_it0.26539432
X-RAY DIFFRACTIONr_scangle_it0.4954.58900
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 6.612→6.784 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.477 17 -
Rwork0.576 389 -
obs--49.82 %

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