Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP

Journal of Inorganic Biochemistry

Volumn 100, Issue 5-6, 2006, Pages 1041-1052

  Sen, Sanchayita ^a   Krishnakumar, Arathi ^a   McClead, Jammi ^b   Johnson, Michael K ^c   Seefeldt, Lance C ^b   Szilagyi, Robert K ^a   Peters, John W ^a  

^a MONTANA STATE UNIVERSITY   (United States)

^b UTAH STATE UNIVERSITY   (United States)

^c UNIVERSITY OF GEORGIA   (United States)

Author keywords

Electron transfer; Fe protein; MgATP; Nitrogenase; Protein conformational change; Signal transduction

Indexed keywords

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE MAGNESIUM; ALUMINUM DERIVATIVE; IRON; LEUCINE; MAGNESIUM ION; NITROGENASE; NUCLEOTIDE; PROTEIN DERIVATIVE;

AMINO ACID SEQUENCE; ARTICLE; CATALYSIS; CLUSTER ANALYSIS; COMPARATIVE STUDY; CONFORMATIONAL TRANSITION; DENSITY FUNCTIONAL THEORY; ELECTRON TRANSPORT; ENZYME BINDING; ENZYME CONFORMATION; ENZYME MECHANISM; ENZYME STABILITY; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; ENZYME SUBUNIT; GENE DELETION; HYDROLYSIS; MOLECULAR INTERACTION; MOLECULE; PROTEIN VARIANT;

ADENOSINE TRIPHOSPHATE; CATALYSIS; LEUCINE; NITROGENASE; PROTEIN CONFORMATION; SEQUENCE DELETION;

EID: 33646157488     PISSN: 01620134     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jinorgbio.2006.02.016     Document Type: Article

References (60)

1. Benton P.M.C., Sen S., and Peters J.W. In: Leigh G.J. (Ed). Nitrogen Fixation at the Millennium (2002), Elsevier, London 36-56
2. Rees D.C., and Howard J.B. Curr. Opin. Chem. Biol. 4 (2000) 559-566
3. Barney B.M., Igarashi R.Y., Dos Santos P.C., Dean D.R., and Seefeldt L.C. J. Biol. Chem 279 (2004) 53621-53624
4. Barney B.M., Laryukhin M., Igarashi R.Y., Lee H.I., Dos Santos P.C., Yang T.C., Hoffman B.M., Dean D.R., and Seefeldt L.C. Biochemistry 44 (2005) 8030-8037
5. Igarashi R.Y., Dos Santos P.C., Niehaus W.G., Dance I.G., Dean D.R., and Seefeldt L.C. J. Biol. Chem. 279 (2004) 34770-34775
6. Seefeldt L.C., Dance I.G., and Dean D.R. Biochemistry 43 (2004) 1401-1409
7. Howard J.B., and Rees D.C. Annu. Rev. Biochem. 63 (1994) 235-264
8. Seefeldt L.C., and Dean D.R. Acc. Chem. Res. 30 (1997) 260-266
9. Burgess B.K., and Lowe D.J. Chem. Rev. 96 (1996) 2983-3012
10. Lowe D.J., and Thorneley R.N.F. Biochem. J. 224 (1984) 895-901
11. Lowe D.J., and Thorneley R.N.F. Biochem. J. 224 (1984) 903-909
12. Lowe D.J., and Thorneley R.N.F. Biochem. J. 224 (1984) 887-894
13. Lowe D.J., and Thorneley R.N.F. Biochem. J. 224 (1984) 877-886
14. Deits T.L., and Howard J.B. J. Biol. Chem. 264 (1989) 6619-6628
15. Ljones T., and Burris R.H. Biochemistry 17 (1978) 1866-1872
16. Walker G.A., and Mortenson L.E. Biochem. Biophys. Res. Commun. 53 (1973) 904-909
17. Walker G.A., and Mortenson L.E. Biochemistry 13 (1974) 2382-2388
18. Chen L., Gavini N., Tsuruta H., Eliezer D., Burgess B.K., Doniach S., and Hodgson K.O. J. Biol. Chem. 269 (1994) 3290-3294
19. Chiu H.J., Peters J.W., Lanzilotta W.N., Ryle M.J., Seefeldt L.C., Howard J.B., and Rees D.C. Biochemistry 40 (2001) 641-650
20. Schindelin H., Kisker C., Schlessman J.L., Howard J.B., and Rees D.C. Nature 387 (1997) 370-376
21. Schmid B., Einsle O., Chiu H.J., Willing A., Yoshida M., Howard J.B., and Rees D.C. Biochemistry 41 (2002) 15557-15565
22. Tezcan F.A., Kaiser J.T., Mustafi D., Walton M.Y., Howard J.B., and Rees D.C. Science 309 (2005) 1377-1380
23. Sen S., Igarashi R., Smith A., Johnson M.K., Seefeldt L.C., and Peters J.W. Biochemistry 43 (2004) 1787-1797
24. Lanzilotta W.N., Fisher K., and Seefeldt L.C. Biochemistry 35 (1996) 7188-7196
25. Ryle M.J., and Seefeldt L.C. Biochemistry 35 (1996) 4766-4775
26. Duyvis M.G., Wassink H., and Haaker H. FEBS Lett. 380 (1996) 233-236
27. Renner K.A., and Howard J.B. Biochemistry 35 (1996) 5353-5358
28. Niu S.Q., Wang X.B., Yang X., Wang L.S., and Ichiye T. J. Phys. Chem. A 108 (2004) 6750-6757
29. Yang X., Wang X.B., Niu S.Q., Pickett C.J., Ichiye T., and Wang L.S. Phys. Rev. Lett. 89 (2002) 1-4
30. Yang X., Wang X.B., and Wang L.S. Int. J. Mass Spectrom. 228 (2003) 797-805
31. Fu Y.J., Niu S.Q., Ichiye T., and Wang L.S. Inorg. Chem. 44 (2005) 1202-1204
32. Niu S.Q., Wang X.B., Nichols J.A., Wang L.S., and Ichiye T. J. Phys. Chem. A 107 (2003) 2898-2907
33. Ryle M.J., Lanzilotta W.N., and Seefeldt L.C. Biochemistry 35 (1996) 9424-9434
34. A.J.W. Leslie, Joint CCP4 and ESF-EACBM newsletter on protein crystallography, 1992.
35. Collaborative Computational Project. Acta Cryst. D 50 (1994) 760-763
36. Jones T., Zou J., and Cowan S. Acta Cryst. D 54 (1991) 905-921
37. Brunger A.T., Adams P.D., and Rice L.M. Curr. Opin. Struct. Biol. 8 (1998) 606-611
38. Brunger A.T., Kuriyan J., and Karplus M. Science 235 (1987) 458-460
39. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. J. Appl. Cryst 26 (1993) 283-291
40. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, J.A. Montgomery, T. Vreven Jr., K.N. Kudin, J.C. Burant, J.M. Millam, S.S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G.A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J.E. Knox, H.P. Hratchian, J.B. Cross, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C, Pomelli, J.W. Ochterski, P.Y. Ayala, K. Morokuma, G.A. Voth, P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S. Dapprich, A.D. Daniels, M.C. Strain, O. Farkas, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Clifford, J. Cioslowski, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, C. Gonzalez, J.A. Pople, Gaussian, Inc., Pittsburgh, PA, 2004.
41. Becke A.D. Phys. Rev. A 38 (1988) 3098-3100
42. Perdew J.P. Phys. Rev. B 33 (1986) 8822-8824
43. Curtiss L.A., McGrath M.P., Blaudeau J.P., Davis N.E., Binning R.C.J., and Radom L. J. Chem. Phys. 103 (1995) 6104-6113
44. Rassolov V.A., Pople J.A., Ratner M.A., and Windus T.L. J. Chem. Phys. 109 (1998) 1223-1229
45. Ryde U., Olsson M.H.M., and Pierloot K. Theor. Comput. Chem. 9 (2001) 1-55
46. Siegbahn P.E.M., and Blomberg M.R.A. Chem. Rev. 100 (2000) 421-437
47. Szilagyi R.K., Metz M., and Solomon E.I. J. Chem. Phys. A 106 (2002) 2994-3007
48. Torres R.A., Lovell T., Noodleman L., and Case D.A. J. Am. Chem. Soc. 125 (2003) 1923-1936
49. Schlegel H.B. J. Comput. Chem. 3 (1982) 214-218
50. Schlegel H.B. In: Yarkony D.R. (Ed). Modern Electronic Structure Theory (1995), World Scientific, Singapore
51. R.K. Szilagyi, M. Winslow, J. Comput. Chem. (submitted).
52. Noodleman L., Lovell T., Han W.G., Li J., and Himo F. Chem. Rev. 104 (2004) 459-508
53. Georgiadis M.M., Komiya H., Chakrabarti P., Woo D., Kornuc J.J., and Rees D.C. Science 257 (1992) 1653-1659
54. Schlessman J.L., Woo D., Joshua-Tor L., Howard J.B., and Rees D.C. J. Mol. Biol. 280 (1998) 669-685
55. Jang S.B., Seefeldt L.C., and Peters J.W. Biochemistry 39 (2000) 14745-14752
56. Chiu H., Peters J.W., Lanzilotta W.N., Ryle M.J., Seefeldt L.C., Howard J.B., and Rees D.C. Biochemistry 40 (2001) 641-650
57. Lanzilotta W.N., Parker V.D., and Seefeldt L.C. Biochim. Biophys. Acta 1429 (1999) 411-421
58. Jang S.B., Jeong M.S., Seefeldt L.C., and Peters J.W. J. Biol. Inorg. Chem. 9 (2004) 1028-1033
59. Lanzilotta W.N., Ryle M.J., and Seefeldt L.C. Biochemistry 34 (1995) 10713-10723
60. Johnson D.C., Dean D.R., Smith A.D., and Johnson M.K. Annu. Rev. Biochem. 74 (2005) 247-281