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The aim of this study was to apply protein structural homology to gain insights into a candidate protein of unknown function (CT398) within the medically important, obligate intracellular bacterium <jats:italic>Chlamydia trachomatis<\/jats:italic>. <jats:italic>C. trachomatis<\/jats:italic> is a major human pathogen responsible for numerous infections throughout the world that can lead to blindness and infertility. A 2.12 \u00c5 crystal structure of hypothetical protein CT398 was determined that was comprised of N\u2010terminal coiled\u2010coil and C\u2010terminal Zn\u2010ribbon domains. The structure of CT398 displayed a high degree of structural similarity to FlgZ (<jats:styled-content>Fl<\/jats:styled-content>a<jats:styled-content>g<\/jats:styled-content>ellar\u2010associated <jats:styled-content>z<\/jats:styled-content>inc\u2010ribbon domain protein) from <jats:italic>Helicobacter pylori<\/jats:italic>. This observation directed analyses of candidate protein partners of CT398, revealing interactions with two paralogous type III secretion system (T3SS) ATPase\u2010regulators (CdsL and FliH) and the alternative sigma factor RpoN (\u03c3<jats:sup>54<\/jats:sup>). Furthermore, genetic introduction of a conditional expression, affinity\u2010tagged construct into <jats:italic>C. trachomatis<\/jats:italic> enabled the purification of a CT398\u2010RpoN\u2010holoenzyme complex, suggesting a potential role for CT398 in modulating transcriptional activity during infection. The interactions reported here, in tandem with previous FlgZ studies in <jats:italic>H. pylori<\/jats:italic>, indicate that CT398 functions as a regulator of several key areas of chlamydial biology throughout the developmental cycle. Accordingly, we propose that CT398 be named CdsZ (<jats:styled-content>C<\/jats:styled-content>ontact\u2010<jats:styled-content>d<\/jats:styled-content>ependent <jats:styled-content>s<\/jats:styled-content>ecretion\u2010associated <jats:styled-content>z<\/jats:styled-content>inc\u2010ribbon domain protein).<\/jats:p>","DOI":"10.1002\/pro.2746","type":"journal-article","created":{"date-parts":[[2015,7,15]],"date-time":"2015-07-15T09:08:47Z","timestamp":1436951327000},"page":"1617-1632","source":"Crossref","is-referenced-by-count":15,"title":["Hypothetical protein <scp>CT<\/scp>398 (<scp>C<\/scp>ds<scp>Z<\/scp>) interacts with \u03c3<sup>54<\/sup> (<scp>R<\/scp>po<scp>N<\/scp>)\u2010holoenzyme and the type III secretion export apparatus in <i>Chlamydia trachomatis<\/i>"],"prefix":"10.1002","volume":"24","author":[{"given":"Michael L.","family":"Barta","sequence":"first","affiliation":[{"name":"Department of Molecular Biosciences University of Kansas Lawrence KS 66045"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin P.","family":"Battaile","sequence":"additional","affiliation":[{"name":"IMCA\u2010CAT, Hauptman\u2010Woodward Medical Research Institute Argonne Illinois"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott","family":"Lovell","sequence":"additional","affiliation":[{"name":"Protein Structure Laboratory Del Shankel Structural Biology Center, University of Kansas Lawrence KS 66045"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P. 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