{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T05:08:50Z","timestamp":1789535330435,"version":"build-2803163510"},"reference-count":50,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2005,1,18]],"date-time":"2005-01-18T00:00:00Z","timestamp":1106006400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Proteins"],"published-print":{"date-parts":[[2005,3]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The protein YbiV from <jats:italic>Escherichia coli<\/jats:italic> K12 MG1655 is a hypothetical protein with sequence homology to the haloacid dehalogenase (HAD) superfamily of proteins. Although numerous members of this family have been identified, the functions of few are known. Using the crystal structure, sequence analysis, and biochemical assays, we have characterized YbiV as a HAD phosphatase. The crystal structure of YbiV reveals a two\u2010domain protein, one with the characteristic HAD hydrolase fold, the other an inserted \u03b1\/\u03b2 fold. In an effort to understand the mechanism, we also solved and report the structures of YbiV in complex with beryllofluoride (BeF<jats:sub>3<\/jats:sub><jats:sup>\u2212<\/jats:sup>) and aluminum trifluoride (AlF<jats:sub>3<\/jats:sub>), which have been shown to mimic the phosphorylated intermediate and transition state for hydrolysis, respectively, in analogy to other HAD phosphatases. Analysis of the structures reveals the substrate\u2010binding cavity, which is hydrophilic in nature. Both structure and sequence homology indicate YbiV may be a sugar phosphatase, which is supported by biochemical assays that measured the release of free phosphate on a number of sugar\u2010like substrates. We also investigated available genomic and functional data in an effort to determine the physiological substrate. Proteins 2005. \u00a9 2005 Wiley\u2010Liss, Inc.<\/jats:p>","DOI":"10.1002\/prot.20267","type":"journal-article","created":{"date-parts":[[2005,1,18]],"date-time":"2005-01-18T21:17:18Z","timestamp":1106083038000},"page":"790-801","source":"Crossref","is-referenced-by-count":31,"title":["Ybiv from <i>Escherichia coli<\/i> K12 is a HAD phosphatase"],"prefix":"10.1002","volume":"58","author":[{"given":"Anne","family":"Roberts","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seok\u2010Yong","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emma","family":"McCullagh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruth E.","family":"Silversmith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David E.","family":"Wemmer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2005,1,18]]},"reference":[{"key":"e_1_2_7_2_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi011405e"},{"key":"e_1_2_7_3_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1994.1711"},{"key":"e_1_2_7_4_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.273.23.14107"},{"key":"e_1_2_7_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(02)00324-8"},{"key":"e_1_2_7_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/35015017"},{"key":"e_1_2_7_7_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi0202373"},{"key":"e_1_2_7_8_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10057"},{"key":"e_1_2_7_9_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M301983200"},{"key":"e_1_2_7_10_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi001171j"},{"key":"e_1_2_7_11_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.271.34.20322"},{"key":"e_1_2_7_12_2","doi-asserted-by":"publisher","DOI":"10.1110\/ps.0302703"},{"key":"e_1_2_7_13_2","doi-asserted-by":"publisher","DOI":"10.1038\/nsb846"},{"key":"e_1_2_7_14_2","first-page":"42","article-title":"Structure and function\u2010based characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum","author":"Kim Y","year":"2003","journal-title":"J Biol Chem"},{"key":"e_1_2_7_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0969-2126(00)00558-X"},{"key":"e_1_2_7_16_2","doi-asserted-by":"publisher","DOI":"10.1093\/emboj\/17.20.6061"},{"key":"e_1_2_7_17_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.60"},{"key":"e_1_2_7_18_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/30.1.56"},{"key":"e_1_2_7_19_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/29.1.72"},{"key":"e_1_2_7_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.174.3.889-898.1992"},{"key":"e_1_2_7_21_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.26.14789"},{"key":"e_1_2_7_22_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0076-6879(97)76075-0"},{"key":"e_1_2_7_23_2","series-title":"Processing of X\u2010ray diffraction data collected in oscillation mode","first-page":"307","author":"Otwinowski Z","year":"1997"},{"key":"e_1_2_7_24_2","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444999000839"},{"key":"e_1_2_7_25_2","series-title":"Methods in enzymology, macromolecular crystallography","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1016\/S0076-6879(97)76073-7","author":"La Fortelle E","year":"1997"},{"key":"e_1_2_7_26_2","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444900005072"},{"key":"e_1_2_7_27_2","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444902018036"},{"key":"e_1_2_7_28_2","doi-asserted-by":"publisher","DOI":"10.1107\/S0108767390010224"},{"key":"e_1_2_7_29_2","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444998003254"},{"key":"e_1_2_7_30_2","doi-asserted-by":"publisher","DOI":"10.1107\/S0021889892009944"},{"key":"e_1_2_7_31_2","first-page":"869","article-title":"MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures","volume":"50","author":"Kraulis EA","year":"1991","journal-title":"J Appl Crystallogr"},{"key":"e_1_2_7_32_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0076-6879(97)77028-9"},{"key":"e_1_2_7_33_2","unstructured":"DeLanoWL. 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