Crystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 at 1.52A resolution.

Experimental Data Snapshot

  • Resolution: 1.52 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

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Structural basis for substrate recognition and processive cleavage mechanisms of the trimeric exonuclease PhoExo I

Miyazono, K.Ishino, S.Tsutsumi, K.Ito, T.Ishino, Y.Tanokura, M.

(2015) Nucleic Acids Res 43: 7122-7136

  • DOI: https://doi.org/10.1093/nar/gkv654
  • Primary Citation of Related Structures:  
    4YOR, 4YOT, 4YOU, 4YOV, 4YOW, 4YOX, 4YOY

  • PubMed Abstract: 

    Nucleases play important roles in nucleic acid processes, such as replication, repair and recombination. Recently, we identified a novel single-strand specific 3'-5' exonuclease, PfuExo I, from the hyperthermophilic archaeon Pyrococcus furiosus, which may be involved in the Thermococcales-specific DNA repair system. PfuExo I forms a trimer and cleaves single-stranded DNA at every two nucleotides. Here, we report the structural basis for the cleavage mechanism of this novel exonuclease family. A structural analysis of PhoExo I, the homologous enzyme from P. horikoshii OT3, showed that PhoExo I utilizes an RNase H-like active site and possesses a 3'-OH recognition site ∼9 Å away from the active site, which enables cleavage at every two nucleotides. Analyses of the heterotrimeric and monomeric PhoExo I activities showed that trimerization is indispensable for its processive cleavage mechanism, but only one active site of the trimer is required.

  • Organizational Affiliation

    Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-5 exonuclease PhoExo I
A, B
229Pyrococcus horikoshiiMutation(s): 0 
Gene Names: HA331_07515
Find proteins for A0A060P168 (Pyrococcus horikoshii)
Explore A0A060P168 
Go to UniProtKB:  A0A060P168
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A060P168
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.52 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.065α = 90
b = 112.065β = 90
c = 202.282γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science, and TechnologyJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-09-16
    Changes: Database references
  • Version 1.2: 2020-02-05
    Changes: Data collection, Database references, Derived calculations