{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T21:31:28Z","timestamp":1781731888032,"version":"3.54.5"},"reference-count":29,"publisher":"Wiley","issue":"7","license":[{"start":{"date-parts":[[2016,4,7]],"date-time":"2016-04-07T00:00:00Z","timestamp":1459987200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"name":"Danish National Research Foundation's Centre for Bacterial Stress Response and Persistence (BASP), Lundbeck Foundation, a Chinese Scholarship Council graduate program"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Proteins"],"published-print":{"date-parts":[[2016,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title><jats:p>The VapC toxin from the <jats:italic>Shigella flexneri<\/jats:italic> 2a virulence plasmid pMYSH6000 belongs to the PIN domain protein family, which is characterized by a conserved fold with low amino acid sequence conservation. The toxin is a <jats:italic>bona fide<\/jats:italic> Mg<jats:sup>2+<\/jats:sup>\u2010dependent ribonuclease and has been shown to target initiator tRNA<jats:sup>fMet<\/jats:sup> <jats:italic>in vivo<\/jats:italic>. Here, we present crystal structures of active site catalytic triad mutants D7A, D7N, and D98N of the VapC toxin in absence of antitoxin. In all structures, as well as in solution, VapC forms a dimer. In the D98N structure, a Hepes molecule occupies both active sites of the dimer and comparison with the structure of RNase H bound to a DNA\/RNA hybrid suggests that the Hepes molecule mimics the position of an RNA nucleotide in the VapC active site. Proteins 2016; 84:892\u2013899. \u00a9 2016 Wiley Periodicals, Inc.<\/jats:p>","DOI":"10.1002\/prot.25002","type":"journal-article","created":{"date-parts":[[2016,2,2]],"date-time":"2016-02-02T08:16:57Z","timestamp":1454401017000},"page":"892-899","source":"Crossref","is-referenced-by-count":16,"title":["Structural analysis of the active site architecture of the VapC toxin from <i><scp>S<\/scp>higella flexneri<\/i>"],"prefix":"10.1002","volume":"84","author":[{"given":"Kehan","family":"Xu","sequence":"first","affiliation":[{"name":"Department of Molecular Biology and Genetics Aarhus University, Gustav Wieds Vej 10c Aarhus C DK\u20108000 Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emil","family":"Dedic","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Genetics Aarhus University, Gustav Wieds Vej 10c Aarhus C DK\u20108000 Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ditlev E.","family":"Brodersen","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Genetics Aarhus University, Gustav Wieds Vej 10c Aarhus C DK\u20108000 Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2016,4,7]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki201"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro1147"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00958-07"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-genet-110410-132412"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.2012.02496.x"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/nchembio.1062"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2010.10.006"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.3390\/toxins6031002"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1100186108"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/protein\/gzq081"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1019587108"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1107\/S1744309113014012"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444909047337"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1107\/S0021889807021206"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2011.10.024"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444912001308"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.22048"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jsb.2014.10.002"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt568"},{"key":"e_1_2_10_21_1","article-title":"Stepwise analyses of metal ions in RNaseH catalysis from substrate destablization to product release","author":"Yang W.","year":"2006","journal-title":"EMBO J"},{"key":"e_1_2_10_22_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M805061200"},{"key":"e_1_2_10_23_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0960-9822(00)00858-7"},{"key":"e_1_2_10_24_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2005.04.024"},{"key":"e_1_2_10_25_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M605198200"},{"key":"e_1_2_10_26_1","doi-asserted-by":"publisher","DOI":"10.1107\/S1744309105012406"},{"key":"e_1_2_10_27_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.20090"},{"key":"e_1_2_10_28_1","doi-asserted-by":"publisher","DOI":"10.1261\/rna.040808.113"},{"key":"e_1_2_10_29_1","doi-asserted-by":"crossref","unstructured":"GlavanF Behm\u2010AnsmantI IzaurraldeE ContiE.Structures of the PIN domains of SMG6 and SMG5 reveal a nuclease within the mRNA surveillance complex. 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