A Surface Loop Directs Conformational Switching of a Lipoyl Domain Between a Folded and a Novel Misfolded Structure

Structure

Volumn 17, Issue 8, 2009, Pages 1117-1127

  Stott, Katherine M ^a   Yusof, Adlina M ^a   Perham, Richard N ^a   Jones, D Dafydd ^a,b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b CARDIFF UNIVERSITY   (United Kingdom)

Author keywords

PROTEINS

Indexed keywords

DIHYDROLIPOAMIDE ACETYLTRANSFERASE; PYRUVATE DEHYDROGENASE;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN QUATERNARY STRUCTURE; PROTEIN STRUCTURE; TEMPERATURE;

AMINO ACID SEQUENCE; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; LIPIDS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN MULTIMERIZATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PYRUVATE DEHYDROGENASE COMPLEX; SEQUENCE HOMOLOGY, AMINO ACID; TEMPERATURE;

ESCHERICHIA COLI;

EID: 68149138669     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2009.07.001     Document Type: Article

References (51)

1. Anfinsen C.B. Principles that govern the folding of protein chains. Science 181 (1973) 223-230
2. Athappilly F.K., and Hendrickson W.A. Structure of the biotinyl domain of acetyl-coenzyme A carboxylase determined by MAD phasing. Structure 3 (1995) 1407-1419
3. Barrientos L.G., Louis J.M., Botos I., Mori T., Han Z., O'Keefe B.R., Boyd M.R., Wlodawer A., and Gronenborn A.M. The domain-swapped dimer of cyanovirin-N is in a metastable folded state: Reconciliation of X-ray and NMR structures. Structure 10 (2002) 673-686
4. Berg A., Vervoort J., and deKok A. Three-dimensional structure in solution of the N-terminal lipoyl domain of the pyruvate dehydrogenase complex from Azotobacter vinelandii. Eur. J. Biochem. 244 (1997) 352-360
5. Berg A., Westphal A.H., Bosma H.J., and de Kok A. Kinetics and specificity of reductive acylation of wild-type and mutated lipoyl domains of 2-oxo-acid dehydrogenase complexes from Azotobacter vinelandii. Eur. J. Biochem. 252 (1998) 45-50
6. Brockwell D.J., Paci E., Zinober R.C., Beddard G.S., Olmsted P.D., Smith D.A., Perham R.N., and Radford S.E. Pulling geometry defines the mechanical resistance of a beta-sheet protein. Nat. Struct. Biol. 10 (2003) 731-737
7. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S., et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54 (1998) 905-921
8. Byeon I.J., Louis J.M., and Gronenborn A.M. A protein contortionist: core mutations of GB1 that induce dimerisation and domain swapping. J. Mol. Biol. 333 (2003) 141-152
9. Cavanagh J., Fairbrother W., Palmer A., Rance M., and Skelton N. Protein NMR Spectroscopy: Principles and Practice. Second Edition (2007), Academic Press, London
10. Chang C.F., Chou H.T., Chuang J.L., Chuang D.T., and Huang T.H. Solution structure and dynamics of the lipoic acid-bearing domain of human mitochondrial branched-chain alpha-keto acid dehydrogenase complex. J. Biol. Chem. 277 (2002) 15865-15873
11. Chiti F., and Dobson C.M. Protein misfolding, functional amyloid, and human disease. Annu. Rev. Biochem. 75 (2006) 333-366
12. Chothia C., and Murzin A.G. New folds for all-β proteins. Structure 1 (1993) 217-222
13. Chothia C., Hubard T., Brenner S., Barns H., and Murzin A. Annu. Rev. Biophys. Biomol. Struct. 26 (1997) 597-627
14. Cornilescu G., Delaglio F., and Bax A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13 (1999) 289-302
15. Cronan J.E., Zhao X., and Jiang Y. Function, attachment and synthesis of lipoic acid in Escherichia coli. Adv. Microb. Physiol. 50 (2005) 103-146
16. Dardel F., Davis A.L., Laue E.D., and Perham R.N. Three dimensional structure of the lipoyl domain from Bacillus stearothermophilus pyruvate dehydrogenase multienzyme complex. J. Mol. Biol. 229 (1993) 1037-1048
17. 1H-NMR assignments and secondary structure of the lipoyl domain of the Bacillus stearothermophilus pyruvate dehydrogenase multienzyme complex. Eur. J. Biochem. 201 (1991) 203-209
18. de Kok A., Hengeveld A.F., Martin A., and Westphal A.H. The pyruvate dehydrogenase multi-enzyme complex from Gram-negative bacteria. Biochim. Biophys. Acta 1385 (1998) 353-366
19. Dobson C.M. Protein folding and misfolding. Nature 426 (2003) 884-890
20. 15N NMR relaxation. Biochemistry 33 (1994) 5984-6003
21. Kirsten Frank M., Dyda F., Dobrodumov A., and Gronenborn A.M. Core mutations switch monomeric protein GB1 into an intertwined tetramer. Nat. Struct. Biol. 9 (2002) 877-885
22. Fries M., Stott K.M., Reynolds S., and Perham R.N. Distinct modes of recognition of the lipoyl domain as substrate by the E1 and E3 components of the pyruvate dehydrogenase multienzyme complex. J. Mol. Biol. 366 (2007) 132-139
23. Gibbs S.J., and Johnson C.S. A PFG NMR experiment for accurate diffusion and flow studies in the presence of eddy currents. J. Magn. Reson. 93 (1991) 395-404
24. Jahn T.R., and Radford S.E. The Yin and Yang of protein folding. FEBS J. 272 (2005) 5962-5970
25. Jones D.D., and Perham R.N. The role of loop and β-turn residues as structural and functional determinants for the lipoyl domain from the Escherichia coli 2-oxoglutarate dehydrogenase complex. Biochem. J. 409 (2008) 357-366
26. Jones D.D., Horne H.J., Reche P.A., and Perham R.N. Structural determinants of post-translational modification and catalytic specificity for the lipoyl domains of the pyruvate dehydrogenase multienzyme complex of Escherichia coli. J. Mol. Biol. 295 (2000) 289-306
27. Jones D.D., Stott K.M., Howard M.J., and Perham R.N. Restricted motion of the lipoyl-lysine swinging arm in the pyruvate dehydrogenase complex of Escherichia coli. Biochemistry 39 (2000) 8448-8459
28. Jones D.D., Stott K.M., Reche P.A., and Perham R.N. Recognition of the lipoyl domain is the ultimate determinant of substrate channelling in the pyruvate dehydrogenase multienzyme complex. J. Mol. Biol. 305 (2001) 49-60
29. Jones J.A., Wilkins D.K., Smith L.J., and Dobson C.M. Characterisation of protein unfolding by NMR diffusion measurements. J. Biomol. NMR 10 (1997) 199-203
30. Kraulis P.J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structure. J. Appl. Cryst. 24 (1991) 946-950
31. Laskowski R.A., Macarthur M.W., Moss D.S., and Thornton J.M. Procheck-a program to check the stereochemical quality of protein structures. J. App. Crystallogra. 26 (1993) 283-291
32. Linge J.P., Habeck M., Rieping W., and Nilges M. ARIA: automated NOE assignment and NMR structure calculation. Bioinformatics 19 (2003) 315-316
33. Liu Y., and Eisenberg D. 3D domain swapping: as domains continue to swap. Protein Sci. 11 (2002) 1285-1299
34. Merritt E.A., and Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277 (1997) 505-524
35. Naik M.T., and Huang T.H. Conformational stability and thermodynamic characterization of the lipoic acid bearing domain of human mitochondrial branched chain alpha-ketoacid dehydrogenase. Protein Sci. 13 (2004) 2483-2492
36. Naik M.T., Chang Y.C., and Huang T.H. Folding kinetics of the lipoic acid-bearing domain of human mitochondrial branched chain alpha-ketoacid dehydrogenase complex. FEBS Lett. 530 (2002) 133-138
37. Newcomer M.E. Protein folding and three-dimensional domain swapping: a strained relationship?. Curr. Opin. Struct. Biol. 12 (2002) 48-53
38. O'Neill J.W., Kim D.E., Johnsen K., Baker D., and Zhang K.Y. Single-site mutations induce 3D domain swapping in the B1 domain of protein L from Peptostreptococcus magnus. Structure 9 (2001) 1017-1027
39. Pares S., Cohen-Addad C., Sieker L., Neuburger M., and Douce R. X-ray structure determination at 2.6-A resolution of a lipoate-containing protein: the H-protein of the glycine decarboxylase complex from pea leaves. Proc. Natl. Acad. Sci. USA 91 (1994) 4850-4853
40. Perham R.N. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu. Rev. Biochem. 69 (2000) 961-1004
41. Perham R.N., Jones D.D., Chauhan H.J., and Howard M.J. Substrate channelling in 2-oxo acid dehydrogenase multienzyme complexes. Biochem. Soc. Trans. 30 (2002) 47-51
42. Piotto M., Saudek V., and Sklenar V. Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J. Biomol. NMR 2 (1992) 661-665
43. Roberts E.L., Shu N., Howard M.J., Broadhurst R.W., Chapman-Smith A., Wallace J.C., Morris T., Cronan Jr. J.E., and Perham R.N. Solution structures of apo and holo biotinyl domains from acetyl coenzyme A carboxylase of Escherichia coli determined by triple-resonance nuclear magnetic resonance spectroscopy. Biochemistry 38 (1999) 5045-5053
44. Rousseau F., Schymkowitz J.W., and Itzhaki L.S. The unfolding story of three-dimensional domain swapping. Structure 11 (2003) 243-251
45. Sambashivan S., Liu Y., Sawaya M.R., Gingery M., and Eisenberg D. Amyloid-like fibrils of ribonuclease A with three-dimensional domain-swapped and native-like structure. Nature 437 (2005) 266-269
46. Tillett M.L., Horsfield M.A., Lian L.Y., and Norwood T.J. Protein-ligand interactions measured by 15N-filtered diffusion experiments. J. Biomol. NMR 13 (1999) 223-232
47. Vranken W.F., Boucher W., Stevens T.J., Fogh R.H., Pajon A., Llinas M., Ulrich E.L., Markley J.L., Ionides J., and Laue E.D. The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59 (2005) 687-696
48. Wallis N.G., Allen M.D., Broadhurst R.W., Lessard I.A., and Perham R.N. Recognition of a surface loop of the lipoyl domain underlies substrate channelling in the pyruvate dehydrogenase multienzyme complex. J. Mol. Biol. 263 (1996) 463-474
49. Wells J.A., and McClendon C.L. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450 (2007) 1001-1009
50. 13C chemical-shift data. J. Biomol. NMR 4 (1994) 171-180
51. Zuiderweg E.R. Mapping protein-protein interactions in solution by NMR spectroscopy. Biochemistry 41 (2002) 1-7