4YOW

Crystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 in complex with poly-dC

Summary for 4YOW

• Entry DOI: 10.2210/pdb4yow/pdb
• Related: 4YOR 4YOT 4YOU 4YOV 4YOX 4YOY
• Descriptor: 3-5 exonuclease PhoExo I, 5'-D(*CP*CP*CP*CP*CP*CP*C)-3' (3 entities in total)
• Functional Keywords: exonuclease, hydrolase-dna complex, hydrolase/dna
• Biological source: Pyrococcus horikoshii; More
• Total number of polymer chains: 6
• Total formula weight: 84595.79

Authors

Miyazono, K.,Ito, T.,Tanokura, M. (deposition date: 2015-03-12, release date: 2015-07-15, Last modification date: 2024-03-20)

Primary citation

Miyazono, K.,Ishino, S.,Tsutsumi, K.,Ito, T.,Ishino, Y.,Tanokura, M.
Structural basis for substrate recognition and processive cleavage mechanisms of the trimeric exonuclease PhoExo I
Nucleic Acids Res., 43:7122-7136, 2015

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.

PubMed: 26138487
DOI: 10.1093/nar/gkv654

Experimental method

X-RAY DIFFRACTION (2.5 Å)