5D1Y

Low resolution crystal structure of human ribonucleotide reductase alpha6 hexamer in complex with dATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 9.005 Å
  • R-Value Free: 0.426 
  • R-Value Work: 0.405 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Allosteric Inhibition of Human Ribonucleotide Reductase by dATP Entails the Stabilization of a Hexamer.

Ando, N.Li, H.Brignole, E.J.Thompson, S.McLaughlin, M.I.Page, J.E.Asturias, F.J.Stubbe, J.Drennan, C.L.

(2016) Biochemistry 55: 373-381

  • DOI: 10.1021/acs.biochem.5b01207

  • PubMed Abstract: 
  • Ribonucleotide reductases (RNRs) are responsible for all de novo biosynthesis of DNA precursors in nature by catalyzing the conversion of ribonucleotides to deoxyribonucleotides. Because of its essential role in cell division, human RNR is a target f ...

    Ribonucleotide reductases (RNRs) are responsible for all de novo biosynthesis of DNA precursors in nature by catalyzing the conversion of ribonucleotides to deoxyribonucleotides. Because of its essential role in cell division, human RNR is a target for a number of anticancer drugs in clinical use. Like other class Ia RNRs, human RNR requires both a radical-generation subunit (β) and nucleotide-binding subunit (α) for activity. Because of their complex dependence on allosteric effectors, however, the active and inactive quaternary forms of many class Ia RNRs have remained in question. Here, we present an X-ray crystal structure of the human α subunit in the presence of inhibiting levels of dATP, depicting a ring-shaped hexamer (α6) where the active sites line the inner hole. Surprisingly, our small-angle X-ray scattering (SAXS) results indicate that human α forms a similar hexamer in the presence of ATP, an activating effector. In both cases, α6 is assembled from dimers (α2) without a previously proposed tetramer intermediate (α4). However, we show with SAXS and electron microscopy that at millimolar ATP, the ATP-induced α6 can further interconvert with higher-order filaments. Differences in the dATP- and ATP-induced α6 were further examined by SAXS in the presence of the β subunit and by activity assays as a function of ATP or dATP. Together, these results suggest that dATP-induced α6 is more stable than the ATP-induced α6 and that stabilization of this ring-shaped configuration provides a mechanism to prevent access of the β subunit to the active site of α.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, California 92037, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonucleoside-diphosphate reductase large subunit
A, B
812Homo sapiensMutation(s): 0 
Gene Names: RRM1 (RR1)
EC: 1.17.4.1
Find proteins for P23921 (Homo sapiens)
Go to Gene View: RRM1
Go to UniProtKB:  P23921
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 9.005 Å
  • R-Value Free: 0.426 
  • R-Value Work: 0.405 
  • Space Group: P 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 356.010α = 90.00
b = 356.010β = 90.00
c = 356.010γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata scaling
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDMR-0936384
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM-103485
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesK99GM100008
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR00GM100008
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM29595

Revision History 

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-01-27
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description
  • Version 1.3: 2017-11-22
    Type: Advisory
  • Version 1.4: 2019-11-27
    Type: Author supporting evidence