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Structure of Escherichia coli uracil-DNA glycosylase and its complexes with nonhydrolyzable substrate analogues in solution studied by synchrotron small-angle X-ray scattering

  • Molecular Biophysics
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Abstract

The structure of native and modified uracil-DNA glycosylase from E. coli in solution was studied by synchrotron small-angle X-ray scattering. The modified enzyme (6His-uracil glycosylase) differs from the native one by the presence of an additional N-terminal 11-meric sequence of amino acid residues, including a block of six His residues. In contrast to minimal differences in the amino acid sequences and functional activity, conformations of native and 6His-uracil glycosylases in solution were found to differ substantially at moderate ionic strength (60 mM NaCl). The structure of uracil-DNA glycosylase in solution is close to that in crystal and shows a tendency toward association. The interaction of this enzyme with nonhydrolyzable analogues of DNA ligands causes partial dissociation of associates and compaction of protein structure. At the same time, 6His-uracil DNA glycosylase has a compact structure, intrinsically different from that in crystals. A decrease in the ionic strength of solution results in a partial destruction of the compact structure of the modified protein, keeping its functional activity unchanged.

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Abbreviations

UDH:

uracil-DNA glycosylase

6His-UDH:

modified UDH

6SSAXS:

synchrotron small angle diffuse X-ray scattering

XRDA:

X-ray diffraction analysis

nU:

2′-amino-2′-deoxyuridine

PDB:

Protein Data Bank

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Authors and Affiliations

  1. Institute of Protein Research, Pushchino, Moscow oblast, 142290, Russia

    A. A. Timchenko

  2. Belozersky Institute of Physicochemical Biology and Faculty of Chemistry, Moscow State University, Vorob’evy gory, Moscow, 119899, Russia

    E. A. Kubareva, E. M. Volkov & M. A. Timchenko

  3. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninskii pr. 33, Moscow, 119071, Russia

    O. L. Voronina

  4. Institute of Agricultural Biotechnology, Russian Academy of Agricultural Sciences, Moscow, 127550, Russia

    V. G. Lunin

  5. Institute of Molecular Biology and Biophysics, Siberian Division, Russian Academy of Medical Sciences, Novosibirsk, 630117, Russia

    D. A. Gonchar & S. Kh. Degtyarev

  6. Physics Laboratory, Kansai Medical University Uyamahigashi, Hirakata Osaka, 573-1136, Japan

    H. Kihara

  7. Department of Biochemistry, Dokkyo University, Mibu, Tochigi, 321-0200, Japan

    K. Kimura

Authors
  1. A. A. Timchenko
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  2. E. A. Kubareva
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  3. E. M. Volkov
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  4. O. L. Voronina
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  5. V. G. Lunin
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  6. D. A. Gonchar
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  7. S. Kh. Degtyarev
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  8. M. A. Timchenko
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  9. H. Kihara
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  10. K. Kimura
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Additional information

Original Russian Text © A.A. Timchenko, E.A. Kubareva, E.M. Volkov, O.L. Voronina, V.G. Lunin, D.A. Gonchar, S.Kh. Degtyarev, M.A. Timchenko, H. Kihara, K. Kimura, 2006, published in Biofizika, 2006, Vol. 51, No. 1, pp. 5–12.

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Timchenko, A.A., Kubareva, E.A., Volkov, E.M. et al. Structure of Escherichia coli uracil-DNA glycosylase and its complexes with nonhydrolyzable substrate analogues in solution studied by synchrotron small-angle X-ray scattering. BIOPHYSICS 51, 1–7 (2006). https://doi.org/10.1134/S0006350906010015

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  • DOI: https://doi.org/10.1134/S0006350906010015

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