Remote phosphate contacts trigger assembly of the active site of DNA topoisomerase IB Journal Article
| Authors: | Tian, L.; Claeboe, C. D.; Hecht, S. M.; Shuman, S. |
| Article Title: | Remote phosphate contacts trigger assembly of the active site of DNA topoisomerase IB |
| Abstract: | Vaccinia topoisomerase IB forms a covalent DNA-(3′-phosphotyrosyl)- enzyme intermediate at its target site 5′-CCCTTp↓ in duplex DNA. The contributions of backbone electrostatics and individual phosphate oxygens to the transesterification reaction were probed by introducing 22 single Rp and Sp methylphosphonate diastereomers at 11 positions flanking the cleavage site. Methyl groups at eight positions (four on the scissile strand and four on the nonscissile strand) inhibited the rate of single-turnover cleavage by factors of 50-50,000. Stereospecific interference was observed at several phosphates, thereby distinguishing simple electrostatic contributions from putative specific polar contacts to either the pro-Sp or pro-Rp oxygens. The functionally relevant phosphate oxygens are located on the minor groove face of the helix on which the scissile phosphodiester resides. Our findings, combined with available crystal structures of vaccinia and human topoisomerase IB, show how specific phosphate contacts remote from where chemistry occurs are critical for assembly of the active site. |
| Keywords: | oxygen; molecular sequence data; base sequence; binding site; crystal structure; models, molecular; binding sites; nucleic acid conformation; phosphate; phosphates; molecular probe; transesterification; electricity; stereochemistry; dna cleavage; dna topoisomerase; dna topoisomerases, type i; organophosphorus compounds; vaccinia; diastereoisomer; nucleotides; methyl group; methylphosphonic acid; humans; priority journal; article |
| Journal Title: | Structure |
| Volume: | 12 |
| Issue: | 1 |
| ISSN: | 0969-2126 |
| Publisher: | Cell Press |
| Date Published: | 2004-01-01 |
| Start Page: | 31 |
| End Page: | 40 |
| Language: | English |
| DOI: | 10.1016/j.str.2003.11.025 |
| PROVIDER: | scopus |
| PUBMED: | 14725763 |
| DOI/URL: | |
| Notes: | Structure -- Cited By (since 1996):30 -- Export Date: 16 June 2014 -- CODEN: STRUE -- Source: Scopus |
Altmetric
Citation Impact
BMJ Impact Analytics
Related MSK Work