3igc | pdb_00003igc

Smallpox virus topoisomerase-DNA transition state

spinqualitylabelsall models 3igc, resolution 2.10Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3igc is a 4 chain structure with sequence from Varv. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: VO4 Gene: H6R, I6R, TOP1 (VARV) Activity: DNA topoisomerase, with EC number 5.99.1.2 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [TOP1_VAR67] Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at the specific target site 5'-[CT]CCTTp site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(3'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 5'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 5'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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. Insights from the structure of a smallpox virus topoisomerase-DNA transition state mimic.,Perry K, Hwang Y, Bushman FD, Van Duyne GD Structure. 2010 Jan 13;18(1):127-37. PMID:20152159 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Smallpox (Variola Virus) - Topoisomerase 1B Topoisomerase Variola Topoisomerase 1B

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