Ligand-induced conformational changes and a reaction intermediate in branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8, as revealed by x-ray crystallography

Journal of Molecular Biology

Volumn 337, Issue 4, 2004, Pages 1011-1033

  Nakai, Tadashi ^a,b   Nakagawa, Noriko ^a   Maoka, Nobuko ^a   Masui, Ryoji ^a,b   Kuramitsu, Seiki ^a,b   Kamiya, Nobuo ^a  

^a RIKEN HARIMA INSTITUTE   (Japan)

^b OSAKA UNIVERSITY   (Japan)

Author keywords

2 oxoisovalerate dehydrogenase; ASA, accessible surface area; BCDH, BCOA dehydrogenase; BCOA, branched chain 2 oxo acid; Covalent intermediate; E1apo, E1 apoenzyme; Induced fit; Michaelis complex; ketoacid dehydrogenase

Indexed keywords

2 OXOISOVALERATE DEHYDROGENASE (LIPOAMIDE);

ARTICLE; CHEMICAL ANALYSIS; CHEMICAL REACTION; CONTROLLED STUDY; CRYSTALLIZATION; DECARBOXYLATION; ENZYME DEGRADATION; ESCHERICHIA COLI; HYDROPHOBICITY; LIGAND BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTON TRANSPORT; THERMUS THERMOPHILUS; X RAY CRYSTALLOGRAPHY;

ESCHERICHIA COLI; THERMUS; THERMUS THERMOPHILUS;

EID: 1642355234     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.02.011     Document Type: Article

References (49)

1. Perham R.N. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu. Rev. Biochem. 69:2000;961-1004.
2. Menkes J.H., Hurst P.L., Craig J.M. A new syndrome: progressive familial infantile cerebral dysfunction associated with an unusual urinary substrate. Pediatrics. 14:1954;462-466.
3. Ævarsson A., Seger K., Turley S., Sokatch J.R., Hol W.G. Crystal structure of 2-oxoisovalerate and dehydrogenase and the architecture of 2-oxo acid dehydrogenase multienzyme complexes. Nature Struct. Biol. 6:1999;785-792.
4. Ævarsson A., Chuang J.L., Wynn R.M., Turley S., Chuang D.T., Hol W.G. Crystal structure of human branched-chain α-ketoacid dehydrogenase and the molecular basis of multienzyme complex deficiency in maple syrup urine disease. Struct. Fold. Des. 8:2000;277-291.
5. Chabrière E., Charon M.H., Volbeda A., Pieulle L., Hatchikian E.C., Fontecilla-Camps J.C. Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate. Nature Struct. Biol. 6:1999;182-190.
6. Muller Y.A., Lindqvist Y., Furey W., Schulz G.E., Jordan F., Schneider G. A thiamin diphosphate binding fold revealed by comparison of the crystal structures of transketolase, pyruvate oxidase and pyruvate decarboxylase. Structure. 1:1993;95-103.
7. Lindqvist Y., Schneider G., Ermler U., Sundström M. Three-dimensional structure of transketolase, a thiamine diphosphate dependent enzyme, at 2.5 Å resolution. EMBO J. 11:1992;2373-2379.
8. Kleiger G., Perry J., Eisenberg D. 3D structure and significance of the GΦXXG helix packing motif in tetramers of the E1β subunit of pyruvate dehydrogenase from the archeon Pyrobaculum aerophilum. Biochemistry. 40:2001;14484-14492.
9. Arjunan P., Nemeria N., Brunskill A., Chandrasekhar K., Sax M., Yan Y., et al. Structure of the pyruvate dehydrogenase multienzyme complex E1 component from Escherichia coli at 1.85 Å resolution. Biochemistry. 41:2002;5213-5221.
10. Ciszak E.M., Korotchkina L.G., Dominiak P.M., Sidhu S., Patel M.S. Structural basis for flip-flop action of thiamin pyrophosphate-dependent enzymes revealed by human pyruvate dehydrogenase. J. Biol. Chem. 278:2003;21240-21246.
11. Dyda F., Furey W., Swaminathan S., Sax M., Farrenkopf B., Jordan F. Catalytic centers in the thiamin diphosphate dependent enzyme pyruvate decarboxylase at 2.4-Å resolution. Biochemistry. 32:1993;6165-6170.
12. Dobritzsch D., König S., Schneider G., Lu G. High resolution crystal structure of pyruvate decarboxylase from Zymomonas mobilis. Implications for substrate activation in pyruvate decarboxylases. J. Biol. Chem. 273:1998;20196-20204.
13. Muller Y.A., Schulz G.E. Structure of the thiamine- and flavin-dependent enzyme pyruvate oxidase. Science. 259:1993;965-967.
14. Hasson M.S., Muscate A., McLeish M.J., Polovnikova L.S., Gerlt J.A., Kenyon G.L., et al. The crystal structure of benzoylformate decarboxylase at 1. 6 Å resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes. Biochemistry. 37:1998;9918-9930.
15. Pang S.S., Duggleby R.G., Guddat L.W. Crystal structure of yeast acetohydroxyacid synthase: a target for herbicidal inhibitors. J. Mol. Biol. 317:2002;249-262.
16. Sundström M., Lindqvist Y., Schneider G. Three-dimensional structure of apotransketolase. Flexible loops at the active site enable cofactor binding. FEBS Letters. 313:1992;229-231.
17. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1993;123-138.
18. Sandalova T., Lindqvist Y. Crystal structure of apo-glycolate oxidase. FEBS Letters. 327:1993;361-365.
19. Hawkins C.F., Borges A., Perham R.N. A common structural motif in thiamin pyrophosphate-binding enzymes. FEBS Letters. 255:1989;77-82.
20. Fiedler E., Thorell S., Sandalova T., Golbik R., König S., Schneider G. Snapshot of a key intermediate in enzymatic thiamin catalysis: crystal structure of the α-carbanion of (α,β-dihydroxyethyl)- thiamin diphosphate in the active site of transketolase from Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA. 99:2002;591-595.
21. Gerstein M., Krebs W. A database of macromolecular motions. Nucl. Acids Res. 26:1998;4280-4290.
22. Jencks W.P. Catalysis in Chemistry and Enzymology. 1969;McGraw-Hill, New York.
23. a during catalysis. Biochemistry. 37:1998;15076-15085.
24. Schellenberger A. Sixty years of thiamin diphosphate biochemistry. Biochim. Biophys. Acta. 1385:1998;177-186.
25. Kern D., Kern G., Neef H., Tittmann K., Killenberg-Jabs M., Wikner C., et al. How thiamine diphosphate is activated in enzymes. Science. 275:1997;67-70.
26. Hübner G., Tittmann K., Killenberg-Jabs M., Schäffner J., Spinka M., Neef H., et al. Activation of thiamin diphosphate in enzymes. Biochim. Biophys. Acta. 1385:1998;221-228.
27. Frey P.A., Flournoy D.S., Gruys K., Yang Y.S. Intermediates in reductive transacetylation catalyzed by pyruvate dehydrogenase complex. Ann. NY Acad. Sci. 573:1989;21-35.
28. Pan K., Jordan F. D,L-S-methyllipoic acid methyl ester, a kinetically viable model for S-protonated lipoic acid as the oxidizing agent in reductive acyl transfers catalyzed by the 2-oxoacid dehydrogenase multienzyme complexes. Biochemistry. 37:1998;1357-1364.
29. + ion-binding site residues in human mitochondrial branched-chain α-ketoacid decarboxylase/dehydrogenase. J. Biol. Chem. 276:2001;4168-4174.
30. 2) E1 component of 2-oxo acid dehydrogenase multienzyme complexes. Biochemistry. 42:2003;6996-7002.
31. Fribourg S., Romier C., Werten S., Gangloff Y.G., Poterszman A., Moras D. Dissecting the interaction network of multiprotein complexes by pairwise coexpression of subunits in E. coli. J. Mol. Biol. 306:2001;363-373.
32. Nakai T., Nakagawa N., Maoka N., Masui R., Kuramitsu S., Kamiya N. Coexpression, purification, crystallization and preliminary X-ray characterization of glycine decarboxylase (P-protein) of the glycine-cleavage system from Thermus thermophilus HB8. Acta Crystallog. sect. D. 59:2003;554-557.
33. Yokoyama S., Hirota H., Kigawa T., Yabuki T., Shirouzu M., Terada T., et al. Structural genomics projects in Japan. Nature Struct. Biol. 7:2000;943-945.
34. Chang A.C., Cohen S.N. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J. Bacteriol. 134:1978;1141-1156.
35. Adachi S., Oguchi T., Tanida H., Park S.Y., Shimizu H., Miyatake H., et al. The RIKEN structural biology beamline II (BL44B2) at the SPring-8. Nucl. Instrum. Methods Phys. Res. sect. A. 467:2001;711-714.
36. Yamamoto M., Kumasaka T., Fujisawa T., Ueki T. Trichromatic concept at SPring-8 RIKEN beamline I. J. Synchrot. Radiat. 5:1998;222-225.
37. Yamamoto M., Kumasaka T., Yamazaki H., Sasaki K., Yokozawa Y., Ishikawa T. Development of high-speed imaging plate detector. Nucl. Instrum. Methods Phys. Res. sect. A. 467:2001;1160-1162.
38. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
39. Navaza J. AMoRe: an automated package for molecular replacement. Acta Crystallog. sect. A. 50:1994;157-163.
40. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography& NMR system: a new software suite for macromolecular structure determination. Acta Crystallog. sect. D. 54:1998;905-921.
41. McRee D.E. A visual protein crystallographic software system for X11/XView. J. Mol. Graph. 10:1992;44-46.
42. Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:1983;2577-2637.
43. Laskowski R.A., Macarthur M.W., Moss D.S., Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291.
44. Collaborative Computational Project Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D. 50:1994;760-763.
45. McDonald I.K., Thornton J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238:1994;777-793.
46. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
47. Merritt E.A., Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277:1997;505-524.
48. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:1994;4673-4680.
49. Gouet P., Courcelle E., Stuart D.I., Metoz F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics. 15:1999;305-308.