6A29

Crystal structure of PprA A139R mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Extended structure of pleiotropic DNA repair-promoting protein PprA from Deinococcus radiodurans.

Adachi, M.Shimizu, R.Shibazaki, C.Satoh, K.Fujiwara, S.Arai, S.Narumi, I.Kuroki, R.

(2019) FASEB J 33: 3647-3658

  • DOI: https://doi.org/10.1096/fj.201801506R
  • Primary Citation of Related Structures:  
    6A27, 6A28, 6A29

  • PubMed Abstract: 

    Pleiotropic protein promoting DNA repair A (PprA) is a key protein facilitating the extreme radiation resistance of Deinococcus radiodurans. PprA is a unique protein to the genus Deinococcus and exists as an oligomer ranging from a tetramer to an ∼100-mer depending on protein concentrations. Here, the X-ray crystal structure of PprA was determined to clarify how PprA confers radiation resistance. The tertiary structure of dimeric PprA was elucidated by using mutants obtained with random and site-directed mutagenesis methods (W183R and A139R); these mutants have disabled DNA binding and polymerization functions. Because the mutant A139R and W183R proteins have dimeric assemblies with 2 different interfaces (Interfaces 1 and 2), the linear and oligomerized PprA model was constructed as a left-handed face-to-face periodic screw structure. In addition, the linear structure in solution was confirmed by small-angle scattering experiments. The site-directed mutational analysis identified essential basic amino acids for DNA binding. These analytical data support the hypothesis that a complex assembly of PprA molecules, which are extended and have a screw structure, surrounds and stretches the DNA strand, acting as a novel guide to colocalize the DNA strands for efficient DNA repairs.-Adachi, M., Shimizu, R., Shibazaki, C., Satoh, K., Fujiwara, S., Arai, S., Narumi, I., Kuroki, R. Extended structure of pleiotropic DNA repair-promoting protein PprA from Deinococcus radiodurans.


  • Organizational Affiliation

    Tokai Quantum Beam Science Center, National Institutes for Quantum and Radiological Science and Technology, Tokai, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein PprA
A, B, C, D, E
A, B, C, D, E, F, G, H
284Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 1 
Gene Names: pprADR_A0346
UniProt
Find proteins for O32504 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore O32504 
Go to UniProtKB:  O32504
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO32504
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.19α = 90
b = 272.26β = 98.64
c = 104.887γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan19370046
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan19380054
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanJP16KT0063

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-26
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references