1XJJ

Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dGTP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Structural Mechanism of Allosteric Substrate Specificity Regulation in a Ribonucleotide Reductase

Larsson, K.-M.Jordan, A.Eliasson, R.Reichard, P.Logan, D.T.Nordlund, P.

(2005) Nat Struct Mol Biol 11: 1142-1149

  • DOI: https://doi.org/10.1038/nsmb838
  • Primary Citation of Related Structures:  
    1XJE, 1XJF, 1XJG, 1XJJ, 1XJK, 1XJM, 1XJN

  • PubMed Abstract: 

    Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides into deoxyribonucleotides, which constitute the precursor pools used for DNA synthesis and repair. Imbalances in these pools increase mutational rates and are detrimental to the cell. Balanced precursor pools are maintained primarily through the regulation of the RNR substrate specificity. Here, the molecular mechanism of the allosteric substrate specificity regulation is revealed through the structures of a dimeric coenzyme B12-dependent RNR from Thermotoga maritima, both in complexes with four effector-substrate nucleotide pairs and in three complexes with only effector. The mechanism is based on the flexibility of loop 2, a key structural element, which forms a bridge between the specificity effector and substrate nucleotides. Substrate specificity is achieved as different effectors and their cognate substrates stabilize specific discrete loop 2 conformations. The mechanism of substrate specificity regulation is probably general for most class I and class II RNRs.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ribonucleotide reductase, B12-dependent
A, B
644Thermotoga maritimaMutation(s): 0 
Gene Names: nrdj
EC: 1.17.4.1
UniProt
Find proteins for O33839 (Thermotoga maritima)
Explore O33839 
Go to UniProtKB:  O33839
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO33839
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.07α = 90
b = 123.88β = 103.7
c = 106.3γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DGTClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description