High-syn conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis MR-1 uridine phosphorylase in the free form and in complex with uridine

Acta Crystallographica Section D: Biological Crystallography

Volumn 70, Issue 12, 2014, Pages 3310-3319

  Safonova, Tatyana N ^a   Mikhailov, Sergey N ^b   Veiko, Vladimir P ^a   Mordkovich, Nadezhda N ^a   Manuvera, Valentin A ^c   Alekseev, Cyril S ^b   Kovalchuk, Mikhail V ^d   Popov, Vladimir O ^a,d   Polyakov, Konstantin M ^a,b  

^a BACH INSTITUTE OF BIOCHEMISTRY   (Russian Federation)

^b ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

^c FEDERAL RESEARCH AND CLINICAL CENTER OF PHYSICAL CHEMICAL MEDICINE OF FEDERAL MEDICAL BIOLOGICAL AGENCY   (Russian Federation)

^d KURCHATOV INSTITUTE   (Russian Federation)

Author keywords

atomic resolution; crystallization under microgravity; high syn conformation of uridine; Shewanella oneidensis MR 1; twinning; uridine phosphorylase

Indexed keywords

ESCHERICHIA COLI; SHEWANELLA ONEIDENSIS MR-1;

URIDINE; URIDINE PHOSPHORYLASE;

CHEMISTRY; ENZYME ACTIVE SITE; ENZYMOLOGY; GRAM NEGATIVE INFECTION; HUMAN; METABOLISM; MICROBIOLOGY; PROTEIN CONFORMATION; SHEWANELLA; X RAY CRYSTALLOGRAPHY;

CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; GRAM-NEGATIVE BACTERIAL INFECTIONS; HUMANS; PROTEIN CONFORMATION; SHEWANELLA; URIDINE; URIDINE PHOSPHORYLASE;

EID: 84916899357     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S1399004714024079     Document Type: Article

References (39)

1. Caradoc-Davies, T. T., Cutfield, S. M., Lamont, I. L. and Cutfield, J. F. (2004). J. Mol. Biol. 337, 337-354.
2. Emsley, P. and Cowtan, K. (2004). Acta Cryst. D60, 2126-2132.
3. Erion, M. D., Stoeckler, J. D., Guida, W. C., Walter, R. L. and Ealick, S. E. (1997). Biochemistry, 36, 11735-11748.
4. Gao, X.-F., Huang, X.-R. and Sun, C.-C. (2006). J. Struct. Biol. 154, 20-26.
5. Kabsch, W. (2010). Acta Cryst. D66, 125-132.
6. Kanzaki, A., Takebayashi, Y., Bando, H., Eliason, J. F., Watanabe, S., Miyashita, H., Fukumoto, M., Toi, M. and Uchida, T. (2002). Int. J. Cancer, 97, 631-635.
7. Krenitsky, T. A., Mellors, J. W. and Barclay, R. K. (1965). J. Biol. Chem. 240, 1281-1286.
8. Krissinel, E. and Henrick, K. (2007). J. Mol. Biol. 372, 774-797.
9. Lashkov, A. A., Zhukhlistova, N. E., Gabdoulkhakov, A. H., Shtil, A. A., Efremov, R. G., Betzel, C. and Mikhailov, A. M. (2010). Acta Cryst. D66, 51-60.
10. Lashkov, A. A., Zhukhlistova, N. E., Seregina, T. A., Gabdoulkhakov, A. G. and Mikhailov, A. M. (2011). Crystallogr. Rep. 56, 560-589.
11. Leer, J. C., Hammer-Jespersen, K. and Schwartz, M. (1977). Eur. J. Biochem. 75, 217-224.
12. Lewkowicz, E. S. and Iribarren, A. M. (2006). Curr. Org. Chem. 10, 1197-1215.
13. Li, N., Smith, T. J. and Zong, M.-H. (2010). Biotechnol. Adv. 28, 348-366.
14. Lunin, V. Y. (2012). Acta Cryst. D68, 732-734.
15. McNicholas, S., Potterton, E., Wilson, K. S. and Noble, M. E. M. (2011). Acta Cryst. D67, 386-394.
16. Mikhailopulo, I. A. and Miroshnikov, A. I. (2010). Acta Naturae, 2, 36-59.
17. Mikhailopulo, I. A. and Miroshnikov, A. I. (2011). Mendeleev Commun. 21, 57-68.
18. Mikhailov, S. N., Lysov, Yu. P. and Yakovlev, G. I. (1999). Mol. Biol. (Russia) 33, 340-354.
19. Mikleušević, G., Štefanić, Z., Narczyk, M., Wielgus-Kutrowska, B., Bzowska, A. and Luić, M. (2011). Biochimie, 93, 1610-1622.
20. Miyahara, T., Nakatsuji, H. and Wada, T. (2014). J. Phys. Chem. A, 118, 2931-2941.
21. Mordkovich, N. N., Manuvera, V. A., Veiko, V. P. and Debabov, V. G. (2012). Biotekhnologiia (Mosc.), 1, 21-30.
22. Mordkovich, N. N., Safonova, T. N., Manuvera, V. A., Veiko, V. P., Polyakov, K. M., Alekseev, K. S., Mikhailov, S. N. and Popov, V. O. (2013). Dokl. Biochem. Biophys. 451, 187-189.
23. Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. and Vagin, A. A. (2011). Acta Cryst. D67, 355-367.
24. Padilla, J. E. and Yeates, T. O. (2003). Acta Cryst. D59, 1124-1130.
25. Paul, D., OLeary, S. E., Rajashankar, K., Bu, W., Toms, A., Settembre, E. C., Sanders, J. M., Begley, T. P. and Ealick, S. E. (2010). Biochemistry, 49, 3499-3509.
26. Prokofev, I. I., Lashkov, A. A., Gabdoulkhakov, A. G., Dontsova, M. V., Seregina, T. A., Mironov, A. S., Betzel, C. and Mikhailov, A.M. (2014). Acta Cryst. F70, 60-63.
27. Pugmire, M. J. and Ealick, S. E. (2002). Biochem. J. 361, 1-25.
28. Roosild, T. P., Castronovo, S., Fabbiani, M. and Pizzorno, G. (2009). BMC Struct. Biol. 9, 14.
29. Saenger, W. (1984). Principles of Nucleic Acid Structure. New York: Springer.
30. Safonova, T. N., Mordkovich, N. N., Polyakov, K.M., Manuvera, V. A., Veiko, V. P. and Popov, V. O. (2012). Acta Cryst. F68, 1387-1389.
31. Tran, T. H., Christoffersen, S., Allan, P. W., Parker, W. B., Piškur, J., Serra, I., Terreni, M. and Ealick, S. E. (2011). Biochemistry, 50, 6549-6558.
32. Trofimov, A. A., Polyakov, K.M., Tikhonov, A. V., Bezsudnova, E. Y., Dorovatovskii, P. V., Gumerov, V. M., Ravin, N. V., Skryabin, K. G. and Popov, V. O. (2013). Dokl. Biochem. Biophys. 449, 99-101.
33. Utagawa, T. (1999). J. Mol. Catal. B Enzym. 6, 215-222.
34. Vagin, A. and Teplyakov, A. (2010). Acta Cryst. D66, 22-25.
35. Veiko, V. P., Siprashvili, Z. Z., Ratmanova, K. I., Gulko, L. B., Mironov, A. A., Andriukhina, R. V. and Debabov, V. G. (1994). Dokl. Akad. Nauk, 339, 819-821.
36. Watanabe, S. and Uchida, T. (1995). Biochem. Biophys. Res. Commun. 216, 265-272.
37. Wegner, G. and Jochims, J. C. (1979). Chem. Ber. 112, 1941-1947.
38. Winn, M. D. et al. (2011). Acta Cryst. D67, 235-242.
39. Yeates, T. O. (1988). Acta Cryst. A44, 142-144.