{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["8(3)"],"submitter":["Jayanth N"],"funding":["Council for Scientific and Industrial Research","Department of Biotechnology, Ministry of Science and Technology"],"pubmed_abstract":["<i>E. coli</i> AlkB, a repair enzyme of the dioxygenase family, catalyses the removal of mutagenic methylated nucleotides from the genome. Known for substrate promiscuity, AlkB's catalytic mechanism and conformational changes accompanying substrate binding have been extensively dissected. However, the structural parameters of various substrates governing their recognition by AlkB still remain elusive. In this work, through solution-state vibrational spectra of methylated substrates bound to AlkB in combination with computational analysis, we show that the recognition specificity is dictated by the protonation states of the substrates. Specificity is conferred predominantly through hydrogen bonding and cation-π interactions. Furthermore, we report on the interaction of AlkB with normal, unm"],"journal":["RSC advances"],"pagination":["1281-1291"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9076979"],"repository":["biostudies-literature"],"pubmed_title":["Structural basis for substrate discrimination by <i>E. coli</i> repair enzyme, AlkB."],"pmcid":["PMC9076979"],"pubmed_authors":["Puranik M","Ogirala N","Jayanth N","Yadav A"],"additional_accession":[]},"is_claimable":false,"name":"Structural basis for substrate discrimination by <i>E. coli</i> repair enzyme, AlkB.","description":"<i>E. coli</i> AlkB, a repair enzyme of the dioxygenase family, catalyses the removal of mutagenic methylated nucleotides from the genome. Known for substrate promiscuity, AlkB's catalytic mechanism and conformational changes accompanying substrate binding have been extensively dissected. However, the structural parameters of various substrates governing their recognition by AlkB still remain elusive. In this work, through solution-state vibrational spectra of methylated substrates bound to AlkB in combination with computational analysis, we show that the recognition specificity is dictated by the protonation states of the substrates. Specificity is conferred predominantly through hydrogen bonding and cation-π interactions. Furthermore, we report on the interaction of AlkB with normal, unm","dates":{"release":"2018-01-01T00:00:00Z","publication":"2018 Jan","modification":"2026-05-30T15:25:57.197Z","creation":"2025-04-04T10:01:45.313Z"},"accession":"S-EPMC9076979","cross_references":{"pubmed":["35540905"],"doi":["10.1039/c7ra11333a"]}}