Structures of the apo and holo forms of formate dehydrogenase from the bacterium Moraxella sp. C-1: Towards understanding the mechanism of the closure of the interdomain cleft

Acta Crystallographica Section D: Biological Crystallography

Volumn 65, Issue 12, 2009, Pages 1315-1325

  Shabalin, I G ^a   Filippova, E V ^b,d   Polyakov, K M ^a,b   Sadykhov, E G ^a   Safonova, T N ^a   Tikhonova, T V ^a   Tishkov, V I ^a,c   Popov, V O ^a  

^a BACH INSTITUTE OF BIOCHEMISTRY   (Russian Federation)

^b ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

^c MOSCOW STATE UNIVERSITY   (Russian Federation)

^d NORTHWESTERN UNIVERSITY   (United States)

Author keywords

Apo and holo forms; Dimer interface; Interdomain cleft; NAD+ dependent formate dehydrogenases; Protein conformation

Indexed keywords

APOENZYME; FORMATE DEHYDROGENASE; HOLOENZYME;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; BIOCATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME SPECIFICITY; ENZYMOLOGY; METABOLISM; MOLECULAR GENETICS; MORAXELLA; PROTEIN MULTIMERIZATION; PROTEIN QUATERNARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; APOENZYMES; BINDING SITES; BIOCATALYSIS; CRYSTALLOGRAPHY, X-RAY; FORMATE DEHYDROGENASES; HOLOENZYMES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MORAXELLA; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY;

BACTERIA (MICROORGANISMS); MORAXELLA SP.; PSEUDOMONAS SP. 101;

EID: 71949095378     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444909040773     Document Type: Article

References (37)

1. Bandaria, J. N., Dutta, S., Hill, S. E., Kohen, A. & Cheatum, C. M. (2008). J. Am. Chem. Soc. 130, 22-23.
2. Castillo, R., Oliva, M., Marti, S. & Moliner, V. (2008). J. Phys. Chem. B, 112, 10012-10022.
3. Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760-763.
4. Emsley, P. & Cowtan, K. (2004). Acta Cryst. D60, 2126-2132.
5. Ernst, M., Kaup, B., Muller, M., Bringer-Meyer, S. & Sahm, H. (2005). Appl. Microbiol. Biotechnol. 66, 629-634.
6. Filippova, E. V., Polyakov, K. M., Tikhonova, T. V., Stekhanova, T. N., Boiko, K. M. & Popov, V. O. (2005). Crystallogr. Rep. 50, 796-800.
7. Filippova, E. V., Polyakov, K. M., Tikhonova, T. V., Stekhanova, T. N., Boiko, K. M., Sadykhov, I. G., Tishkov, V. I. & Popov, V. O. (2006). Crystallogr. Rep. 51, 627-631.
8. Folch, B., Rooman, M. & Dehouck, Y. (2007). J. Chem. Inf. Model. 48, 119-127.
9. Hayward, S. & Kitao, A. (2006). Biophys. J. 91, 1823-1831.
10. Kabsch, W. (1993). J. Appl. Cryst. 26, 795-800.
11. Kabsch, W. & Sander, C. (1983). Biopolymers, 22, 2577-2637.
12. Klein, C. & Bartels, K. S. (2000). Acta Cryst. A56, s295.
13. Krissinel, E. & Henrick, K. (2007). J. Mol. Biol. 372, 774-797.
14. Kumar, S., Ma, B., Tsai, C. J., Wolfson, H. & Nussinov, R. (1999). Cell Biochem. Biophys. 31, 141-164.
15. Lamzin, V. S., Asadchikov, V. E., Popov, V. O., Egorov, A. M. & Berezin, I. V. (1986). Dokl. Akad. Nauk SSSR, 291, 1011-1014.
16. Lamzin, V. S., Dauter, Z., Popov, V. O., Harutyunyan, E. H. &Wilson, K. S. (1994). J. Mol. Biol. 236, 759-785.
17. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J. & Higgins, D. G. (2007). Bioinformatics, 23, 2947-2948.
18. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). J. Appl. Cryst. 26, 283-291.
19. Li, W. F., Zhou, X. X. & Lu, P. (2005). Biotechnol. Adv. 23, 271-281.
20. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
21. Popov, V. O. & Lamzin, V. S. (1994). Biochem. J. 301, 625-643.
22. Popov, V. O. & Tishkov, V. I. (2003). Protein Structures: Kaleidoscope of Structural Properties and Functions, edited by V. N. Uversky, pp. 441-473. Kerala, India: Research Signpost.
23. Potterton, L., McNicholas, S., Krissinel, E., Gruber, J., Cowtan, K., Emsley, P., Murshudov, G. N., Cohen, S., Perrakis, A. & Noble, M. (2004). Acta Cryst. D60, 2288-2294.
24. Razeto, A., Kochhar, S., Hottinger, H., Dauter, M., Wilson, K. S. & Lamzin, V. S. (2002). J. Mol. Biol. 318, 109-119.
25. Sadykhov, E. G., Serov, A. E., Voinova, N. S., Uglanova, S. V., Petrov, A. S., Alekseeva, A. A., Kleimenov, S. I., Popov, V. I. & Tishkov, V. I. (2006). Prikl. Biokhim. Mikrobiol. 42, 269-273.
26. Schirwitz, K., Schmidt, A. & Lamzin, V. S. (2007). Protein Sci. 16, 1146-1156.
27. Stillman, T. J.,Migueis, A. M.,Wang, X. G., Baker, P. J., Britton, K. L., Engel, P. C. & Rice, D. W. (1999). J. Mol. Biol. 285, 875-885.
28. Tishkov, V. I. (2009). Personal communication.
29. Tishkov, V. I., Galkin, A. G. & Egorov, A. M. (1991). Dokl. Akad. Nauk SSSR, 317, 745-748.
30. Tishkov, V. I., Galkin, A. G., Fedorchuk, V. V., Savitsky, P. A., Rojkova, A. M., Gieren, H. & Kula, M. R. (1999). Biotechnol. Bioeng. 64, 187-193.
31. Tishkov, V. I., Matorin, A. D., Rojkova, A. M., Fedorchuk, V. V., Savitsky, P. A., Dementieva, L. A., Lamzin, V. S., Mezentzev, A. V. & Popov, V. O. (1996). FEBS Lett. 390, 104-108.
32. Tishkov, V. I. & Popov, V. O. (2004). Biochemistry (Mosc.), 69, 1252-1267.
33. Tishkov, V. I. & Popov, V. O. (2006). Biomol. Eng. 23, 89-110.
34. Torres, R. A., Schitt, B. & Bruice, T. C. (1999). J. Am. Chem. Soc. 121, 8164-8173.
35. Vagin, A. & Teplyakov, A. (1997). J. Appl. Cryst. 30, 1022-1025.
36. Vinals, C., Depiereux, E. & Feytmans, E. (1993). Biochem. Biophys. Res. Commun. 192, 182-188.
37. Weckbecker, A. & Hummel, W. (2004). Biotechnol. Lett. 26, 1739-1744.