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TitleStructural basis for allosteric regulation of human ribonucleotide reductase by nucleotide-induced oligomerization.
Journal, issue, pagesNat Struct Mol Biol, Vol. 18, Issue 3, Page 316-322, Year 2011
Publish dateFeb 20, 2011
AuthorsJames 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 /
PubMed AbstractRibonucleotide 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.
External linksNat Struct Mol Biol / PubMed:21336276 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.3 - 28.0 Å
Structure data

EMDB-1807:
Saccharomyces cerevisiae ribonucleotide reductase hole complex at the presence of dATP
Method: EM (single particle) / Resolution: 28.0 Å

PDB-2wgh:
Human Ribonucleotide reductase R1 subunit (RRM1) in complex with dATP and Mg.
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-3hnc:
Crystal structure of human ribonucleotide reductase 1 bound to the effector TTP
Method: X-RAY DIFFRACTION / Resolution: 2.41 Å

PDB-3hnd:
Crystal structure of human ribonucleotide reductase 1 bound to the effector TTP and substrate GDP
Method: X-RAY DIFFRACTION / Resolution: 3.21 Å

PDB-3hne:
Crystal structure of human ribonucleotide reductase 1 bound to the effectors TTP and ATP
Method: X-RAY DIFFRACTION / Resolution: 3.11 Å

PDB-3hnf:
Crystal structure of human ribonucleotide reductase 1 bound to the effectors TTP and dATP
Method: X-RAY DIFFRACTION / Resolution: 3.16 Å

PDB-3paw:
Low resolution X-ray crystal structure of Yeast Rnr1p with dATP bound in the A-site
Method: X-RAY DIFFRACTION / Resolution: 6.61 Å

Chemicals

ChemComp-GOL:
GLYCEROL

ChemComp-MG:
Unknown entry

ChemComp-DTP:
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

ChemComp-HOH:
WATER

ChemComp-TTP:
THYMIDINE-5'-TRIPHOSPHATE

ChemComp-SO4:
SULFATE ION

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • homo sapiens (human)
KeywordsOXIDOREDUCTASE / DNA REPLICATION / ALLOSTERIC ENZYME / NUCLEOTIDE-BINDING / CYTOPLASM / ATP-BINDING / POLYMORPHISM / ribonucleotide reductase / Nucleotide binding

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