Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15

Han, G.W.; Elsliger, M.-A.; Yeates, T.O.; Xu, Q.; Murzin, A.G.; Krishna, S.S.; Jaroszewski, L.; Abdubek, P.; Astakhova, T.; Axelrod, H.L.; Carlton, D.; Chen, C.; Chiu, H.-J.; Clayton, T.; Das, D.; Deller, M.C.; Duan, L.; Ernst, D.; Feuerhelm, J.; Grant, J.C.; Grzechnik, A.; Jin, K.K.; Johnson, H.A.; Klock, H.E.; Knuth, M.W.; Kozbial, P.; Kumar, A.; Lam, W.W.; Marciano, D.; McMullan, D.; Miller, M.D.; Morse, A.T.; Nigoghossian, E.; Okach, L.; Reyes, R.; Rife, C.L.; Sefcovic, N.; Tien, H.J.; Trame, C.B.; van den Bedem, H.; Weekes, D.; Hodgson, K.O.; Wooley, J.; Deacon, A.M.; Godzik, A.; Lesley, S.A.; Wilson, I.A.

doi:10.1107/S1744309110025534

Figure 5
(a–c) Comparison of the active sites of YP_001813558.1, S. solfataricus MazG and C. jejuni dUTPase. The putative conserved active-site metal-binding residues are shown as stick models. Note that Asp95 in YP_001813558.1 is offset by one residue when compared with the other two structures. No metal was found in YP_001813558.1. One Li⁺ ion (red ball) is bound in MazG based on the crystallization conditions. Three Mg²⁺ ions (red balls) are bound in the C. jejuni dUTPase structure. The nucleotide-binding sites contain either a 1,2-ethanediol (EDO) molecule (YP_001813558.1), an unknown ligand (UNL; S. solfataricus MazG) or 2′-deoxyuridine 5′-α,β-imidodiphosphate (DUN; dUTPase; PDB code 1w2y ) and are represented in red. (d) Comparison of the nucleotide-recognition site in YP_001813558.1 (green), S. solfataricus MazG (light blue) and C. jejuni dUTPase (pink) as a stereoview. The EDO molecule from YP_001813558.1 (red sticks), UNL from S. solfataricus MazG (blue balls) and DUN from C. jejuni dUTPase (purple sticks) are shown. Mse12 is modeled as three conformations in the MazG structure. (e) Stereoview of the superposition of the substrate analogs DUN (purple) from C. jejuni dUTPase and 2-deoxy-5-methylcytidine-5′-(tetrahydrogen triphosphate (yellow) from M. musculus RS21-C6 and the EDO (red) molecule bound to the YP_001813558.1 structure. Hydrogen bonds are shown as dotted lines. The key residues from YP_001813558.1 that are predicted to be involved in substrate binding are presented as a green stick model.

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ISSN: 2053-230X

Volume 66| Part 10| August 2010| Pages 1237-1244

doi:10.1107/S1744309110025534

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