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However, \u03c3<jats:sub>4<\/jats:sub> of \u03c3<jats:sup>70<\/jats:sup> appears to be poorly folded on its own. Here, by fusing \u03c3<jats:sub>4<\/jats:sub> with the RNA polymerase \u03b2\u2010flap\u2010tip\u2010helix, we constructed two \u03c3<jats:sub>4<\/jats:sub> chimera proteins, one from \u03c3<jats:sup>70<\/jats:sup> <jats:inline-graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"graphic\/prot25768-math-0003.png\" xlink:title=\"urn:x-wiley:08873585:media:prot25768:prot25768-math-0003\"\/> and another from \u03c3<jats:sup>S<\/jats:sup> <jats:inline-graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"graphic\/prot25768-math-0004.png\" xlink:title=\"urn:x-wiley:08873585:media:prot25768:prot25768-math-0004\"\/> of <jats:italic>Klebsiella pneumoniae<\/jats:italic>. The two chimera proteins well folded into a monomeric form with strong binding affinities for \u221235 element DNA. Determining the crystal structure of <jats:inline-graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"graphic\/prot25768-math-0005.png\" xlink:title=\"urn:x-wiley:08873585:media:prot25768:prot25768-math-0005\"\/> in complex with \u221235 element DNA revealed that <jats:inline-graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"graphic\/prot25768-math-0006.png\" xlink:title=\"urn:x-wiley:08873585:media:prot25768:prot25768-math-0006\"\/> adopts a similar structure as \u03c3<jats:sub>4<\/jats:sub> in the <jats:italic>Escherichia coli<\/jats:italic> RNA polymerase \u03c3<jats:sup>S<\/jats:sup> holoenzyme and recognizes \u221235 element DNA specifically by several conserved residues from the helix\u2010turn\u2010helix motif. By using nuclear magnetic resonance (NMR), <jats:inline-graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"graphic\/prot25768-math-0007.png\" xlink:title=\"urn:x-wiley:08873585:media:prot25768:prot25768-math-0007\"\/> was demonstrated to recognize \u221235 element DNA similar to <jats:inline-graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"graphic\/prot25768-math-0008.png\" xlink:title=\"urn:x-wiley:08873585:media:prot25768:prot25768-math-0008\"\/>. Carr\u2010Purcell\u2010Meiboom\u2010Gill relaxation dispersion analyses showed that the N\u2010terminal helix and the \u03b2\u2010flap\u2010tip\u2010helix of <jats:inline-graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"graphic\/prot25768-math-0009.png\" xlink:title=\"urn:x-wiley:08873585:media:prot25768:prot25768-math-0009\"\/> have a concurrent transient \u03b1\u2010helical structure and DNA binding reduced the slow dynamics on <jats:inline-graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"graphic\/prot25768-math-0010.png\" xlink:title=\"urn:x-wiley:08873585:media:prot25768:prot25768-math-0010\"\/>. Finally, only <jats:inline-graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"graphic\/prot25768-math-0011.png\" xlink:title=\"urn:x-wiley:08873585:media:prot25768:prot25768-math-0011\"\/> was shown to interact with the response regulator PmrA and its promoter DNA. The chimera proteins are capable of \u221235 element DNA recognition and can be used for study with transcription factors or other factors that interact with domain 4 of \u03c3 factors.<\/jats:p>","DOI":"10.1002\/prot.25768","type":"journal-article","created":{"date-parts":[[2019,7,11]],"date-time":"2019-07-11T07:33:24Z","timestamp":1562830404000},"page":"69-81","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Structural basis for \u221235 element recognition by \u03c3<sub>4<\/sub> chimera proteins and their interactions with PmrA response regulator"],"prefix":"10.1002","volume":"88","author":[{"given":"Yuan\u2010Chao","family":"Lou","sequence":"first","affiliation":[{"name":"Institute of Biomedical Sciences, Academia Sinica  Taipei Taiwan, ROC"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chun\u2010Chi","family":"Chou","sequence":"additional","affiliation":[{"name":"Institute of Biomedical 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