{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T01:45:42Z","timestamp":1770687942730,"version":"3.49.0"},"reference-count":43,"publisher":"Wiley","issue":"7","license":[{"start":{"date-parts":[[2009,1,2]],"date-time":"2009-01-02T00:00:00Z","timestamp":1230854400000},"content-version":"vor","delay-in-days":551,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Protein Science"],"published-print":{"date-parts":[[2007,7]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>In bacteria, the dehydration of 2\u2010methylcitrate to yield 2\u2010methylaconitate in the 2\u2010methylcitric acid cycle is catalyzed by a cofactor\u2010less (PrpD) enzyme or by an aconitase\u2010like (AcnD) enzyme. Bacteria that use AcnD also require the function of the PrpF protein, whose function was previously unknown. To gain insights into the function of PrpF, the three\u2010dimensional crystal structure of the PrpF protein from the bacterium <jats:italic>Shewanella oneidensis<\/jats:italic> was solved at 2.0 \u00c5 resolution. The protein fold of PrpF is strikingly similar to those of the non\u2010PLP\u2010dependent diaminopimelate epimerase from <jats:italic>Haemophilus influenzae<\/jats:italic>, a putative proline racemase from <jats:italic>Brucella melitensis<\/jats:italic>, and to a recently deposited structure of a hypothetical protein from <jats:italic>Pseudomonas aeruginosa<\/jats:italic>. Results from in vitro studies show that PrpF isomerizes <jats:italic>trans<\/jats:italic>\u2010aconitate to <jats:italic>cis<\/jats:italic>\u2010aconitate. It is proposed that PrpF catalysis of the <jats:italic>cis\u2013trans<\/jats:italic> isomerization proceeds through a base\u2010catalyzed proton abstraction coupled with a rotation about C2\u2013C3 bond of 2\u2010methylaconitate, and that residue Lys73 is critical for PrpF function. The newly identified function of PrpF as a non\u2010PLP\u2010dependent isomerase, together with the fact that PrpD\u2010containing bacteria do not require PrpF, suggest that the isomer of 2\u2010methylaconitate that serves as a substrate of aconitase must have the same stereochemistry as that synthesized by PrpD. From this, it follows that the 2\u2010methylaconitate isomer generated by AcnD is not a substrate of aconitase, and that PrpF is required to generate the correct isomer. As a consequence, the isomerase activity of PrpF may now be viewed as an integral part of the 2\u2010methylcitric acid cycle.<\/jats:p>","DOI":"10.1110\/ps.072801907","type":"journal-article","created":{"date-parts":[[2007,6,14]],"date-time":"2007-06-14T04:09:03Z","timestamp":1181794143000},"page":"1274-1284","source":"Crossref","is-referenced-by-count":23,"title":["The three\u2010dimensional crystal structure of the PrpF protein of <i>Shewanella oneidensis<\/i> complexed with <i>trans<\/i>\u2010aconitate: Insights into its biological function"],"prefix":"10.1002","volume":"16","author":[{"given":"Graeme S.","family":"Garvey","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher J.","family":"Rocco","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jorge C.","family":"Escalante\u2010Semerena","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ivan","family":"Rayment","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2009,1,2]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0601635103"},{"key":"e_1_2_6_3_1","volume-title":"Handbook of media for environmental microbiology","author":"Atlas R.","year":"1995"},{"key":"e_1_2_6_4_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1432-1033.1994.tb18718.x"},{"key":"e_1_2_6_5_1","doi-asserted-by":"publisher","DOI":"10.1128\/jb.62.3.293-300.1951"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.186.3.595-600.2004"},{"key":"e_1_2_6_7_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0407371101"},{"key":"e_1_2_6_8_1","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-147-8-2203"},{"key":"e_1_2_6_9_1","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.68.1.271-279.2002"},{"key":"e_1_2_6_10_1","first-page":"278","volume-title":"Biology of the procaryotes","author":"Buckel W.","year":"1999"},{"key":"e_1_2_6_11_1","doi-asserted-by":"publisher","DOI":"10.1021\/bi982138o"},{"key":"e_1_2_6_12_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.184.10.2728-2739.2002"},{"key":"e_1_2_6_13_1","doi-asserted-by":"publisher","DOI":"10.1107\/S0021889897006729"},{"key":"e_1_2_6_14_1","first-page":"101","volume-title":"Human colonic bacteria: Role in nutrition, physiology and pathology","author":"Cummings J.H.","year":"1995"},{"key":"e_1_2_6_15_1","doi-asserted-by":"publisher","DOI":"10.1136\/gut.28.10.1221"},{"key":"e_1_2_6_16_1","volume-title":"The PyMOL molecular graphics system","author":"DeLano W.L.","year":"2002"},{"key":"e_1_2_6_17_1","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444904019158"},{"key":"e_1_2_6_18_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.20025"},{"key":"e_1_2_6_19_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.186.2.454-462.2004"},{"key":"e_1_2_6_20_1","doi-asserted-by":"publisher","DOI":"10.1128\/jb.179.3.928-940.1997"},{"key":"e_1_2_6_21_1","doi-asserted-by":"publisher","DOI":"10.1021\/bi015503b"},{"key":"e_1_2_6_22_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M100244200"},{"key":"e_1_2_6_23_1","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444998012517"},{"key":"e_1_2_6_24_1","doi-asserted-by":"publisher","DOI":"10.1021\/bi00788a012"},{"key":"e_1_2_6_25_1","doi-asserted-by":"publisher","DOI":"10.1021\/bi00788a011"},{"key":"e_1_2_6_26_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-5822.2007.00901.x"},{"key":"e_1_2_6_27_1","doi-asserted-by":"publisher","DOI":"10.1107\/S0021889892009944"},{"key":"e_1_2_6_28_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-6-298"},{"key":"e_1_2_6_29_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.2003.03633.x"},{"key":"e_1_2_6_30_1","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444996012255"},{"key":"e_1_2_6_31_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0076-6879(97)76066-X"},{"key":"e_1_2_6_32_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0602537103"},{"key":"e_1_2_6_33_1","doi-asserted-by":"publisher","DOI":"10.1021\/ja0125321"},{"key":"e_1_2_6_34_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.180.4.767-772.1998"},{"key":"e_1_2_6_35_1","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-148-7-2215"},{"key":"e_1_2_6_36_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0969-2126(98)00037-9"},{"key":"e_1_2_6_37_1","volume-title":"Current protocols in molecular biology","author":"Sasse J.","year":"1991"},{"key":"e_1_2_6_38_1","doi-asserted-by":"publisher","DOI":"10.1110\/ps.041129605"},{"key":"e_1_2_6_39_1","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1080\/00021369.1974.10861293","article-title":"Production of 2\u2010methylisocitric acid from N\u2010paraffins by mutants of candida\u2010lipolytica","volume":"38","author":"Tabuchi T.","year":"1974","journal-title":"Agric. 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