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Structure of a Nudix protein from Pyrobaculum aerophilum reveals a dimer with two intersubunit beta-sheets.

Wang S, Mura C, Sawaya MR, Cascio D, Eisenberg D
Acta Crystallogr D Biol Crystallogr 58 571-8 (2002)
Related entries: 1k26, 1k2e

Cited: 14 times
EuropePMC logo PMID: 11914479

Abstract

Nudix proteins, formerly called MutT homolog proteins, are a large family of proteins that play an important role in reducing the accumulation of potentially toxic compounds inside the cell. They hydrolyze a wide variety of substrates that are mainly composed of a nucleoside diphosphate linked to some other moiety X and thus are called Nudix hydrolases. Here, the crystal structure of a Nudix hydrolase from the hyperthermophilic archaeon Pyrobaculum aerophilum is reported. The structure was determined by the single-wavelength anomalous scattering method with data collected at the peak anomalous wavelength of an iridium-derivatized crystal. It reveals an extensive dimer interface, with each subunit contributing two strands to the beta-sheet of the other subunit. Individual subunits consist of a mixed highly twisted and curved beta-sheet of 11 beta-strands and two alpha-helices, forming an alpha-beta-alpha sandwich. The conserved Nudix box signature motif, which contains the essential catalytic residues, is located at the first alpha-helix and the beta-strand and loop preceding it. The unusually short connections between secondary-structural elements, together with the dimer form of the structure, are likely to contribute to the thermostability of the P. aerophilum Nudix protein.

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  1. De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features. Ward RM, Erdin S, Tran TA, Kristensen DM, Lisewski AM, Lichtarge O. PLoS One 3 e2136 (2008)
  2. Stretching to understand proteins - a survey of the protein data bank. Sułkowska JI, Cieplak M. Biophys J 94 6-13 (2008)


Reviews citing this publication (2)

  1. Structures and mechanisms of Nudix hydrolases. Mildvan AS, Xia Z, Azurmendi HF, Saraswat V, Legler PM, Massiah MA, Gabelli SB, Bianchet MA, Kang LW, Amzel LM. Arch Biochem Biophys 433 129-143 (2005)
  2. Protein production in Escherichia coli for structural studies by X-ray crystallography. Goulding CW, Perry LJ. J Struct Biol 142 133-143 (2003)

Articles citing this publication (10)

  1. The structure of irisin reveals a novel intersubunit β-sheet fibronectin type III (FNIII) dimer: implications for receptor activation. Schumacher MA, Chinnam N, Ohashi T, Shah RS, Erickson HP. J Biol Chem 288 33738-33744 (2013)
  2. The evolution of function within the Nudix homology clan. Srouji JR, Xu A, Park A, Kirsch JF, Brenner SE. Proteins 85 775-811 (2017)
  3. An introduction to biomolecular graphics. Mura C, McCrimmon CM, Vertrees J, Sawaya MR. PLoS Comput Biol 6 e1000918 (2010)
  4. Novel multiprotein complexes identified in the hyperthermophilic archaeon Pyrococcus furiosus by non-denaturing fractionation of the native proteome. Menon AL, Poole FL, Cvetkovic A, Trauger SA, Kalisiak E, Scott JW, Shanmukh S, Praissman J, Jenney FE, Wikoff WR, Apon JV, Siuzdak G, Adams MW, Adams MW. Mol Cell Proteomics 8 735-751 (2009)
  5. Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base. Nakamura T, Meshitsuka S, Kitagawa S, Abe N, Yamada J, Ishino T, Nakano H, Tsuzuki T, Doi T, Kobayashi Y, Fujii S, Sekiguchi M, Yamagata Y. J Biol Chem 285 444-452 (2010)
  6. Structure of a coenzyme A pyrophosphatase from Deinococcus radiodurans: a member of the Nudix family. Kang LW, Gabelli SB, Bianchet MA, Xu WL, Bessman MJ, Amzel LM. J Bacteriol 185 4110-4118 (2003)
  7. Diverse substrate recognition and hydrolysis mechanisms of human NUDT5. Arimori T, Tamaoki H, Nakamura T, Kamiya H, Ikemizu S, Takagi Y, Ishibashi T, Harashima H, Sekiguchi M, Yamagata Y. Nucleic Acids Res 39 8972-8983 (2011)
  8. Structural studies of the Nudix hydrolase DR1025 from Deinococcus radiodurans and its ligand complexes. Ranatunga W, Hill EE, Mooster JL, Holbrook EL, Schulze-Gahmen U, Xu W, Bessman MJ, Brenner SE, Holbrook SR. J Mol Biol 339 103-116 (2004)
  9. Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus. Gabelli SB, Bianchet MA, Azurmendi HF, Xia Z, Sarawat V, Mildvan AS, Amzel LM. Structure 12 927-935 (2004)
  10. Homology modeling and substrate binding study of Nudix hydrolase Ndx1 from Thermos thermophilus HB8. Zheng QC, Li ZS, Sun M, Zhang Y, Sun CC. Biochem Biophys Res Commun 333 881-887 (2005)


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