Domain features of the peripheral stalk subunit H of the methanogenic A1AO ATP synthase and the NMR solution structure of H 1-47

Biophysical Journal

Volumn 97, Issue 1, 2009, Pages 286-294

  Biuković, Goran ^a   Gayen, Shovanlal ^a   Pervushin, Konstantin ^a   Grüber, Gerhard ^a  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

CYSTEINE; PROTEIN SUBUNIT; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CIRCULAR DICHROISM; CROSS LINKING; DIMERIZATION; DISULFIDE BOND; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN DOMAIN; PROTEIN PURIFICATION; PROTEIN STRUCTURE;

ARCHAEAL PROTEINS; ATP SYNTHETASE COMPLEXES; CIRCULAR DICHROISM; DIFFUSION; ELECTROPHORESIS, POLYACRYLAMIDE GEL; METHANOCOCCUS; MODELS, MOLECULAR; MUTATION; NITROGEN ISOTOPES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN SUBUNITS; PROTONS; ULTRAVIOLET RAYS;

EID: 68949136016     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.04.026     Document Type: Article

References (42)

1. Lolkema, J. S., Y. Chaban, and E. J. Boekema. 2003. Subunit composition, structure, and distribution of bacterial V-type ATPase. J. Bioenerg. Biomembr. 35:323-336.
2. +-translocating ATPase from Enterococcus hirae. J. Bioenerg. Biomembr. 37:411-413.
3. O ATPases: structural, functional and mechanistical aspects of an energy producer and an energy transducer. Bioessays. 30:1096-1109.
4. Coskun, Ü ., Y. L. Chaban, A. Lingl, V. Müller, W. Keegstra, et al. 2004. Structure and subunit arrangement of the A-type ATP synthase complex from the archaeon Methanococcus jannaschii visualized by electron microscopy. J. Biol. Chem. 279:38644-38648.
5. +-ATPase/synthase by electron microscopy. Structure. 12:1789-1798.
6. Gayen, S., A. M. Balakrishna, G. Biuković, W. Yulei, and G. Grüber. 2008. Identification of critical residues of subunit H in its interaction with subunit E of the A-ATP synthase from Methanocaldococcus jannaschii. FEBS J. 275:1803-1812.
7. Grüber, G., D. I. Svergun, Ü. Coskun, T. Lemker, M. H. J. Koch, et al. 2000. Structural insights into the A1 ATPase from the archaeon, Methanosarcina mazei Gö1. Biochemistry. 40:1890-1896.
8. Coskun, Ü., M. Radermacher, V. Müller, T. Ruiz, and G. Grüber. 2004. Three-dimensional organization of the archaeal A1-ATPase from Methanosarcina mazei Gö1. J. Biol. Chem. 279:22759-22764.
9. O ATP synthase. J. Bioenerg. Biomembr. 38:83-92.
10. Maegawa, W., H. Morita, D. Iyaguchi, M. Yao, N. Watanabe, et al. 2006. Structure of the catalytic nucleotide-binding subunit A of A-type ATP synthase from Pyrococcus horikoshii reveals a novel domain related to the peripheral stalk. Acta Crystallogr. D Biol. Crystallogr. 62:483-488.
11. O subunits A and B. J. Mol. Biol. 358:725-740.
12. Iwata, M., H. Imamura, E. Stambouli, C. Ikeda, M. Tamakoshi, et al. 2004. Crystal structure of a central stalk subunit C and reversible association/ dissociation of vacuole-type ATPase. Proc. Natl. Acad. Sci. USA. 101:59-64.
13. Numoto, N., A. Kita, and K. Mike. 2004. Structure of the C subunit of V-type ATPase from Thermus themophilus at 1.85 A° resolution. Acta Crystallogr. D Biol. Crystallogr. 60:810-815.
14. O ATP synthase and its interaction with the nucleotide-binding subunit B. Biochemistry. 46:11684-11694.
15. +-ATPase. J. Mol. Biol. 366:933-944.
16. +-ATPase from Enterococcus hirae. Science. 308:654-659.
17. O ATP synthase from Methanocaldococcus jannaschii and its binding to the catalytic A subunit. Biochemistry. 46:2070-2078.
18. Grüber, G., J. Godovac-Zimmermann, T. A. Link, Ü. Coskun, V. F. Rizzo, et al. 2002. Expression, purification and characterization of subunit E, an essential subunit of the vacuolar-ATPase. Biochem. Biophys. Res. Commun. 298:383-391.
19. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 227:680-685.
20. Ho, S. N., H. D. Hunt, R. M. Horton, J. K. Pullen, and L. R. Pease. 1989. Site directed mutagenesis by overlap extension using polymerase chain reaction. Gene. 77:51-59.
21. Manavalan, P., and W. C. Johnson, Jr. 1987. Variable selection method improves the prediction of protein secondary structure from circular dichroism spectra. Anal. Biochem. 167:76-85.
22. Sreerama, N., and R. W. Woody. 1993. A self-consistent method for the analysis of protein secondary structure from circular dichroism. Anal. Biochem. 209:32-44.
23. Provencher, S. W. 1982. A constrained regularization method of inverting data represented by linear algebraic or integral quations. Comput. Phys. Commun. 27:213-227.
24. Andrade, M. A., P. Chacon, J. J. Merelo, and F. Moran. 1993. Evaluation of secondary structure of proteins from UV circular dichroism spectra using an unsupervised learning neural network. Protein Eng. 6:383-390.
25. Deléage, G., and C. Geourjon. 1993. An interactive graphic program for calculating the secondary structures content of proteins from circular dichroism spectrum. Comput. Appl. Biosci. 9:197-199.
26. Böhm, G. 1992. Quantitative analysis of protein far UV circular dichroism spectra by neural networks. Protein Eng. 5:191-195.
27. Sattler, M., J. Schleucher, and C. Griesinger. 1999. Heteronuclear multidimensional NMR experiments for the structure determination of proteins in proteins employing pulsed field gradients. Prog. Nucl. Magn. Reson. Spectrosc. 34:93-158.
28. Delaglio, F., S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer, et al. 1995. NMRPipe: a multidimensional spectral processing system based on UNIX. J. Biomol. NMR. 6:277-293.
29. Kneller, D. G., and T. D. Goddard. 1997. SPARKY 3, 105 ed. University of California, San Francisco, CA.
30. Wüthrich, K. 1986. NMR of Proteins and Nuclei Acids. Wiley Interscience, New York.
31. Herrmann, T., P. Güntert, and K. Wüthrich. 2002. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J. Mol. Biol. 319:209-227.
32. Cornilescu, G., F. Delaglio, and A. Bax. 1999. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR. 13:289-302.
33. Koradi, R., M. Billeter, and K. Wüthrich. 1996. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14:51-55.
34. Palmer, A. G., J. Williams, and A. McDermott. 1996. Nuclear magnetic resonance studies of biopolymer dynamics. J. Phys. Chem. 100:13293-13310.
35. Shaka, A. J., P. B. Barker, and R. Freeman. 1985. Computer optimized decoupling scheme for wideband applications and low-level operation. J. Magn. Reson. 64:547-552.
36. Pervushin, K., G. Wider, and K. Wüthrich. 1997. Deuterium relaxation in a uniformly 15N labelled homeodomain and its DNA complex. J. Am. Chem. Soc. 119:3842-3843.
37. Mandel, A. M., M. Akke, and A. G. Palmer. 1995. Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. J. Mol. Biol. 246:144-163.
38. Cole, R., and J. P. Loria. 2003. FAST-Modelfree: a program for rapid automated analysis of solution NMR spin-relaxation data. J. Biomol. NMR. 26:203-213.
39. Gibbs, S. J., and C. S. J. Johnson. 1969. A PFG NMR experiment for accurate diffusion and flow studies in the presence of eddy currents. J. Magn. Reson. 93:395-402.
40. Wilkins, D. K., S. B. Grimshaw, V. Receveur, C. M. Dobson, J. A. Jones, et al. 1999. Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques. Biochemistry. 38:16424-16431.
41. Lipari, G., and A. Szabo. 1982. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J.J. Am. Chem. Soc. 104:4546-4559.
42. Jarymowycz, V. A., and M. J. Stone. 2006. Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences. Chem. Rev. 106:1624-1671.