Adenylate kinase motions during catalysis: An energetic counterweight balancing substrate binding

Structure

Volumn 4, Issue 2, 1996, Pages 147-156

  Muller C W ^a   Schlauderer, G J ^a   Reinstein, J ^b   Schulz, G E ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

^b MAX PLANCK INSTITUTE OF MOLECULAR PHYSIOLOGY   (Germany)

Author keywords

Adenylate kinase; Energetic counterweight; Induced fit kinematics; Substrate binding; X ray structure

Indexed keywords

ESCHERICHIA COLI;

ADENYLATE KINASE;

ARTICLE; CATALYSIS; CHEMISTRY; ENZYME SPECIFICITY; METABOLISM; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

ADENYLATE KINASE; CATALYSIS; CRYSTALLOGRAPHY, X-RAY; PROTEIN CONFORMATION; SUBSTRATE SPECIFICITY;

EID: 0029644168     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(96)00018-4     Document Type: Article

References (34)

1. Noda, L.H. (1973). In The Enzymes. (Boyer, P.D., ed), vol. 8, pp. 279-305, Academic Press, New York.
2. Dreusicke, D., Karplus, P.A. & Schulz, G.E. (1988). Refined structure of porcine cytosolic adenylate kinase at 2.1 Å resolution. J. Mol. Biol. 199, 359-371.
3. Diederichs, K. & Schulz, G.E. (1991). The refined structure of the complex between adenylate kinase from beef heart mitochondrial matrix and its substrate AMP at 1.85 Å resolution. J. Mol. Biol. 217, 541-549.
4. 5A refined at 1.9 Å resolution. J. Mol. Biol. 224, 159-177.
5. Stehle, T. & Schulz, G.E. (1992), Refined structure of the complex between guanylate kinase and its substrate GMP at 2.0 Å resolution. J. Mol. Biol. 224, 1127-1141.
6. 5A, showing the pathway of phosphoryl transfer. Protein Sci. 4, 1262-1271.
7. Müller-Dieckmann, H.J. & Schulz G.E. (1695). Substrate specificity and assembly of the catalytic center derived from two structures of ligated uridylate kinase. J. Mol. Biol. 246, 522-530.
8. Berry, M.B., et al., & Phillips, N.P., Jr. (1994). The closed conformation of a highly flexible protein: the structure of E. coli adenylate kinase with bound AMP and AMPPNP, Protiens 19, 183-198.
9. Wild, K., Bohner, T., Aubry, A. Folkers, G. &. Schulz, G.E. (1995). The three-dimensional structure of thymidine kinase from Herpes simplex virus type 1. FEBS Lett. 368, 289-292.
10. Schulz, G.E. (1992). Binding of nucleotides by proteins. Curr. Opin. Struct. Biol. 2, 61-67.
11. 1-ATPase from bovine heart mitochondria. Nature 370, 621-628.
12. Rayment, I., et al., & Holden, H.M. (1993). Three-dimensional structure of myosin subfragment-1: a molecular motor. Science 261, 50-58.
13. Dreusicke, D. & Schulz, G.E. (1986). The glycine-rich loop of adenylate kinase forms a giant anion hole. FEBS Lett. 208, 301-304.
14. Schulz, G.E., Müller, C.W. & Diederichs, K. (1990). Induced-fit movements in adenylate kinases. J. Mol. Biol. 213, 627-630.
15. Gerstein, M., Schulz, G.E. <& Chothia, C. (1993). Domain closure in adenylate kinase: joints on either side of two helices close like neighboring fingers. J. Mol. Biol. 229, 494-5011
16. Vonrhein, C., Schlauderer, G.J. & Schulz, G.E. (1995). Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases. Structure 3, 483-490.
17. Reinstein, J., Schlichting, I. & Wittinghofer, A. (1990). Structurally and catalytically important residues in the phosphate binding loop of adenylate kinase of Escherichia coli. Biochemistry 29, 7451-7459.
18. Laskowski, R.A., MacArthur, M.W. & Thornton, J.M. (1994). Evaluation of protein coordinate sets. In From First Map to Final Model. (Bailey, S., Hubbard, R. & Waller, D.A., eds), pp.149-159. SERC Daresbury Laboratory, Warrington, UK.
19. Brünger, A.T., Kuriyan, J. & Karplus, M. (1987). Crystallographic R-factor refinement by molecular dynamics. Science 235, 458-460.
20. Schlauderer, G.J. & Schulz, G.E. (1996). The structure of bovine mitochondrial adenylate kinase, comparison with isoenzymes in other compartments. Protein Sci. 5, in press.
21. Jaeger, I. (1985). Isolation, purification and separation of the adenylate kinase isoenzymes from bovine liver mitochondria and comparison with the enzyme from bovine heart [Diploma thesis]. Albert-Ludwigs-Universität, Freiburg im Breisgau, Germany.
22. Schneemann, A. (1986). Purification, characterization and crystallization of the short and long adenylate kinase variants from the intermembrane space of bovine liver mitochondria [Diploma thesis]. Albert-Ludwigs-Universität, Freiburg im Breisgau, Germany
23. Pai, E.F., Krengel, U., Petsko, G.A., Goody, R.S., Kabsch, W. & Wittinghofer, A. (1990). Refined structure of the triphosphate conformation of H-ras p21 at 1.35 Å resolution: implications for the mechanism of GTP hydrolysis. EMBO J. 9, 2351-2359.
24. βγ, receptors, and effectors. Cell 73, 631-641.
25. iα2 and the mechanism of GTP hydrolysis. Science 265, 1405-1412.
26. Noel, J.P., Hamm, H.E. & Sigler, P.B. (1993). The 2.2 Å crystal structure of transducin-α complexed with GTPγS. Nature 366, 654-663.
27. Dratz, E.A., et al., & Hamm, H.E. (1993). NMR structure of a receptor-bound G-protein peptide. Nature 363, 276-281.
28. Gerstein, M. & Chothia, C. (1991). Analysis of protein loop closure. J. Mol. Biol. 220, 133-149.
29. Brune, M., Schumann, R. & Wittinghofer, A. (1985). Cloning and sequencing of the adenylate kinase gene (ADK) of Escherichia coli. Nucleic Acids Res. 13, 7139-7151.
30. 5-di(adenosine-5′-)pentaphosphate. J. Mol. Biol. 202, 909-912.
31. Kabsch, W. (1988). Evaluation of single crystal X-ray diffraction from a position sensitive detector. J. Appl. Cryst. 21, 916-924.
32. Brünger, A.T. (1990). Extension of molecular replacement: a new search strategy based on Patterson correlation refinement. Acta Cryst. A 46, 46-57.
33. Luzzati, V. (1953). Traitement statistique des erreurs dans la determination des structures crystallines. Acta Cryst. 5, 802-810.
34. Read, R.J. (1986). Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Cryst. A 42, 140-149.