{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1363670319122882176.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.1073/pnas.0610007104"}},{"identifier":{"@type":"URI","@value":"https://pnas.org/doi/pdf/10.1073/pnas.0610007104"}}],"dc:title":[{"@value":"Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase"}],"description":[{"type":"abstract","notation":[{"@value":"<jats:p>\n            Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) constitute an important, yet relatively poorly understood, family of heme-containing enzymes. Here, we report extensive structural and biochemical studies of the\n            <jats:italic>Xanthomonas campestris</jats:italic>\n            TDO and a related protein SO4414 from\n            <jats:italic>Shewanella oneidensis</jats:italic>\n            , including the structure at 1.6-Å resolution of the catalytically active, ferrous form of TDO in a binary complex with the substrate\n            <jats:sc>l</jats:sc>\n            -Trp. The carboxylate and ammonium moieties of tryptophan are recognized by electrostatic and hydrogen-bonding interactions with the enzyme and a propionate group of the heme, thus defining the\n            <jats:sc>l</jats:sc>\n            -stereospecificity. A second, possibly allosteric,\n            <jats:sc>l</jats:sc>\n            -Trp-binding site is present at the tetramer interface. The sixth coordination site of the heme-iron is vacant, providing a dioxygen-binding site that would also involve interactions with the ammonium moiety of\n            <jats:sc>l</jats:sc>\n            -Trp and the amide nitrogen of a glycine residue. The indole ring is positioned correctly for oxygenation at the C2 and C3 atoms. The active site is fully formed only in the binary complex, and biochemical experiments confirm this induced-fit behavior of the enzyme. The active site is completely devoid of water during catalysis, which is supported by our electrochemical studies showing significant stabilization of the enzyme upon substrate binding.\n          </jats:p>"}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1380857624283639045","@type":"Researcher","foaf:name":[{"@value":"Farhad Forouhar"}],"jpcoar:affiliationName":[{"@value":"*Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027;"}]},{"@id":"https://cir.nii.ac.jp/crid/1380857624283639054","@type":"Researcher","foaf:name":[{"@value":"J. L. Ross Anderson"}],"jpcoar:affiliationName":[{"@value":"School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom; and"}]},{"@id":"https://cir.nii.ac.jp/crid/1380857624283639056","@type":"Researcher","foaf:name":[{"@value":"Christopher G. Mowat"}],"jpcoar:affiliationName":[{"@value":"School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom; and"}]},{"@id":"https://cir.nii.ac.jp/crid/1380857624283639040","@type":"Researcher","foaf:name":[{"@value":"Sergey M. Vorobiev"}],"jpcoar:affiliationName":[{"@value":"*Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027;"}]},{"@id":"https://cir.nii.ac.jp/crid/1380857624283639055","@type":"Researcher","foaf:name":[{"@value":"Arif Hussain"}],"jpcoar:affiliationName":[{"@value":"*Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027;"}]},{"@id":"https://cir.nii.ac.jp/crid/1380857624283639043","@type":"Researcher","foaf:name":[{"@value":"Mariam Abashidze"}],"jpcoar:affiliationName":[{"@value":"*Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027;"}]},{"@id":"https://cir.nii.ac.jp/crid/1380857624283639051","@type":"Researcher","foaf:name":[{"@value":"Chiara Bruckmann"}],"jpcoar:affiliationName":[{"@value":"School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom; and"}]},{"@id":"https://cir.nii.ac.jp/crid/1380857624283639050","@type":"Researcher","foaf:name":[{"@value":"Sarah J. Thackray"}],"jpcoar:affiliationName":[{"@value":"School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom; and"}]},{"@id":"https://cir.nii.ac.jp/crid/1380857624283639042","@type":"Researcher","foaf:name":[{"@value":"Jayaraman Seetharaman"}],"jpcoar:affiliationName":[{"@value":"*Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027;"}]},{"@id":"https://cir.nii.ac.jp/crid/1380857624283639052","@type":"Researcher","foaf:name":[{"@value":"Todd Tucker"}],"jpcoar:affiliationName":[{"@value":"*Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027;"}]},{"@id":"https://cir.nii.ac.jp/crid/1380857624283639044","@type":"Researcher","foaf:name":[{"@value":"Rong Xiao"}],"jpcoar:affiliationName":[{"@value":"Center for Advanced Biotechnology and Medicine and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, NJ 08854"}]},{"@id":"https://cir.nii.ac.jp/crid/1380857624283639053","@type":"Researcher","foaf:name":[{"@value":"Li-Chung Ma"}],"jpcoar:affiliationName":[{"@value":"Center for Advanced Biotechnology and Medicine and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, NJ 08854"}]},{"@id":"https://cir.nii.ac.jp/crid/1380857624283639046","@type":"Researcher","foaf:name":[{"@value":"Li Zhao"}],"jpcoar:affiliationName":[{"@value":"Center for Advanced Biotechnology and Medicine and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, NJ 08854"}]},{"@id":"https://cir.nii.ac.jp/crid/1380857624283639048","@type":"Researcher","foaf:name":[{"@value":"Thomas B. Acton"}],"jpcoar:affiliationName":[{"@value":"Center for Advanced Biotechnology and Medicine and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, NJ 08854"}]},{"@id":"https://cir.nii.ac.jp/crid/1380857624283639047","@type":"Researcher","foaf:name":[{"@value":"Gaetano T. Montelione"}],"jpcoar:affiliationName":[{"@value":"Center for Advanced Biotechnology and Medicine and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, NJ 08854"}]},{"@id":"https://cir.nii.ac.jp/crid/1380857624283639049","@type":"Researcher","foaf:name":[{"@value":"Stephen K. Chapman"}],"jpcoar:affiliationName":[{"@value":"School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom; and"}]},{"@id":"https://cir.nii.ac.jp/crid/1380857624283639041","@type":"Researcher","foaf:name":[{"@value":"Liang Tong"}],"jpcoar:affiliationName":[{"@value":"*Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027;"}]}],"publication":{"publicationIdentifier":[{"@type":"PISSN","@value":"00278424"},{"@type":"EISSN","@value":"10916490"}],"prism:publicationName":[{"@value":"Proceedings of the National Academy of Sciences"}],"dc:publisher":[{"@value":"Proceedings of the National Academy of Sciences"}],"prism:publicationDate":"2007-01-09","prism:volume":"104","prism:number":"2","prism:startingPage":"473","prism:endingPage":"478"},"reviewed":"false","url":[{"@id":"https://pnas.org/doi/pdf/10.1073/pnas.0610007104"}],"createdAt":"2006-12-30","modifiedAt":"2022-04-12","relatedProduct":[{"@id":"https://cir.nii.ac.jp/crid/1360285708096225024","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Initial O<sub>2</sub>Insertion Step of the Tryptophan Dioxygenase Reaction Proposed by a Heme-Modification Study"}]},{"@id":"https://cir.nii.ac.jp/crid/1360285708939032960","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Unique coupling of mono- and dioxygenase chemistries in a single active site promotes heme degradation"}]},{"@id":"https://cir.nii.ac.jp/crid/1360567187443738368","@type":"Article","resourceType":"学術雑誌論文(journal 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