Tyrosine 656 in topoisomerase II[beta] is important for the catalytic activity of the enzyme: Identification based on artifactual +80-Da modification at this site

Topoisomerase (topo) II catalyzes topological changes in DNA. Although both human isozymes, topo II[alpha] and [beta] are phosphorylated, site-specific phosphorylation of topo II[beta] is poorly characterized. Using LC-MS/MS analysis of topo II[beta], cleaved with trypsin, Arg C or cyanogen bromide (CNBr) plus trypsin, we detected four +80-Da modified sites: tyr656, ser1395, thr1426 and ser1545. Phosphorylation at ser1395, thr1426 and ser1545 was established based on neutral loss of H3PO4 (-98Da) in the CID spectra and on differences in 2-D-phosphopeptide maps of 32P-labeled wild-type (WT) and S1395A or T1426A/S1545A mutant topo II[beta]. However, phosphorylation at tyr656 could not be verified by 2-D-phosphopeptide mapping of 32P-labeled WT and Y656F mutant protein or by Western blotting with phosphotyrosine-specific antibodies. Since the +80-Da modification on tyr656 was observed exclusively during cleavage with CNBr and trypsin, this modification likely represented bromination, which occurred during CNBr cleavage. Re-evaluation of the CID spectra identified +78/+80-Da fragment ions in CID spectra of two peptides containing tyr656 and tyr711, confirming bromination. Interestingly, mutation of only tyr656, but not ser1395, thr1326 or ser1545, decreased topo II[beta] activity, suggesting a functional role for tyr656. These results, while identifying an important tyrosine in topo II[beta], underscore the importance of careful interpretation of modifications having the same nominal mass. [PUBLICATION ABSTRACT]