3IGC

Smallpox virus topoisomerase-DNA transition state

Summary for 3IGC

• Entry DOI: 10.2210/pdb3igc/pdb
• Descriptor: DNA topoisomerase 1, 5'-D(*GP*TP*GP*TP*CP*GP*CP*CP*CP*TP*T)-3', 5'-D(*AP*TP*TP*CP*C)-3', ... (6 entities in total)
• Functional Keywords: topoisomerase, protein-dna complex, poxvirus, isomerase, atp-binding, dna-binding, late protein, nucleotide-binding, isomerase-dna complex, isomerase/dna
• Biological source: Variola virus (smallpox virus); More
• Total number of polymer chains: 4
• Total formula weight: 46484.80

Authors

Perry, K.,Hwang, Y.,Bushman, F.D.,Van Duyne, G.D. (deposition date: 2009-07-27, release date: 2010-03-02, Last modification date: 2023-09-06)

Primary citation

Perry, K.,Hwang, Y.,Bushman, F.D.,Van Duyne, G.D.
Insights from the Structure of a Smallpox Virus Topoisomerase-DNA Transition State Mimic.
Structure, 18:127-137, 2010

PubMed Abstract: Poxviruses encode their own type IB topoisomerases (TopIBs), which release superhelical tension generated by replication and transcription of their genomes. To investigate the reaction catalyzed by viral TopIBs, we have determined the structure of a variola virus topoisomerase-DNA complex trapped as a vanadate transition state mimic. The structure reveals how the viral TopIB enzymes are likely to position the DNA duplex for ligation following relaxation of supercoils and identifies the sources of friction observed in single-molecule experiments that argue against free rotation. The structure also identifies a conformational change in the leaving group sugar that must occur prior to cleavage and reveals a mechanism for promoting ligation following relaxation of supercoils that involves an Asp-minor groove interaction. Overall, the new structural data support a common catalytic mechanism for the TopIB superfamily but indicate distinct methods for controlling duplex rotation in the small versus large enzyme subfamilies.

PubMed: 20152159
DOI: 10.1016/j.str.2009.10.020

Experimental method

X-RAY DIFFRACTION (2.1 Å)