3HNF

Crystal structure of human ribonucleotide reductase 1 bound to the effectors TTP and dATP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

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This is version 1.2 of the entry. See complete history. 


Literature

Structural basis for allosteric regulation of human ribonucleotide reductase by nucleotide-induced oligomerization.

Fairman, J.W., Wijerathna, S.R., Ahmad, M.F., Xu, H., Nakano, R., Jha, S., Prendergast, J., Welin, R.M., Flodin, S., Roos, A., Nordlund, P., Li, Z., Walz, T., Dealwis, C.G.

(2011) Nat Struct Mol Biol 18: 316-322

  • DOI: 10.1038/nsmb.2007
  • Primary Citation of Related Structures:  
    2WGH, 3HNC, 3HND, 3HNE, 3HNF, 3PAW

  • PubMed 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 for catalysis. RR is allosterically regulated by its activator ATP and its inhibitor dATP, which regulate RR activity by inducing oligomerization of RR1 ...

    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.

    Organizational Affiliation: 

    Department of Biochemistry, University of Tennessee, Knoxville, TN, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase large subunitA, B792Homo sapiensMutation(s): 0 
Gene Names: RR1, RRM1
EC: 1.17.4.1
UniProt & NIH Common Fund Data Resources
Find proteins for P23921 (Homo sapiens)
Explore P23921 
Go to UniProtKB:  P23921
PHAROS:  P23921
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23921
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.856α = 90
b = 114.388β = 90
c = 220.003γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Advisory, Refinement description