Structure-function relations in oxaloacetate decarboxylase complex. Fluorescence and infrared approaches to monitor oxomalonate and Na+ binding effect

PLoS ONE

Volumn 5, Issue 6, 2010, Pages 1-10

  Granjon, Thierry ^a,b   Maniti, Ofelia ^b   Auchli, Yolanda ^a   Dahinden, Pius ^a   Buchet, René ^b   Marcillat, Olivier ^b   Dimroth, Peter ^a  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITÉ LYON 1   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; CARBOXYLYASE; OXALOACETATE DECARBOXYLASE; OXOMALONATE; SODIUM ION; TRYPTOPHAN; UNCLASSIFIED DRUG; MALONIC ACID DERIVATIVE; SODIUM;

ARTICLE; BACTERIAL STRAIN; BIOTINYLATION; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; DECARBOXYLATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME PURIFICATION; ESCHERICHIA COLI; EXCITATION; GENETIC VARIABILITY; HYDROPHOBICITY; NONHUMAN; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; SPECTROSCOPY; STRUCTURE ANALYSIS; CATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; ELECTROCHEMISTRY; INFRARED SPECTROPHOTOMETRY; METABOLISM; METHODOLOGY; SPECTROFLUOROMETRY; STRUCTURE ACTIVITY RELATION;

CARBOXY-LYASES; CATALYSIS; ELECTROCHEMISTRY; MALONATES; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; SODIUM; SPECTROMETRY, FLUORESCENCE; SPECTROPHOTOMETRY, INFRARED; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 77956220997     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0010935     Document Type: Article

References (44)

1. Buckel W (2001) Sodium ion-translocating decarboxylases. Biochim Biophys Acta 1505: 15-27.
2. Dimroth P, Schink B (1998) Energy conservation in the decarboxylation of dicarboxylic acids by fermenting bacteria. Arch Microbiol 170: 69-77.
3. Bott M (1997) Anaerobic citrate metabolism and its regulation in enterobacteria. Arch Microbiol 167: 78-88.
4. Dimroth P (1997) Primary sodium ion translocating enzymes. Biochim Biophys Acta 1318: 11-51.
5. Dimroth P, Thomer A (1983) Subunit composition of oxaloacetate decarboxylase and characterization of the alpha chain as carboxyltransferase. Eur J Biochem 137: 107-112.
6. Dimroth P, Thomer A (1988) Dissociation of the sodium-ion-translocating oxaloacetate decarboxylase of Klebsiella pneumoniae and reconstitution of the active complex from the isolated subunits. Eur J Biochem 175: 175-180.
7. Woehlke G, Wifling K, Dimroth P (1992) Sequence of the sodium ion pump oxaloacetate decarboxylase from Salmonella typhimurium. J Biol Chem 267: 22798-22803.
8. Dahinden P, Pos KM, Dimroth P (2005) Identification of a domain in the alphasubunit of the oxaloacetate decarboxylase Na+ pump that accomplishes complex formation with the gamma-subunit. Febs J 272: 846-855.
9. Studer R, Dahinden P, Wang WW, Auchli Y, Li XD, et al. (2007) Crystal structure of the carboxyltransferase domain of the oxaloacetate decarboxylase Na+ pump from Vibrio cholerae. J Mol Biol 367: 547-557.
10. Hall PR, Zheng R, Antony L, Pusztai-Carey M, Carey PR, et al. (2004) Transcarboxylase 5S structures: assembly and catalytic mechanism of a multienzyme complex subunit. Embo J 23: 3621-3631.
11. Jockel P, Schmid M, Choinowski T, Dimroth P (2000) Essential role of tyrosine 229 of the oxaloacetate decarboxylase beta-subunit in the energy coupling mechanism of the Na(+) pump. Biochemistry 39: 4320-4326.
12. Jockel P, Schmid M, Steuber J, Dimroth P (2000) A molecular coupling mechanism for the oxaloacetate decarboxylase Na+ pump as inferred from mutational analysis. Biochemistry 39: 2307-2315.
13. Schmid M, Wild MR, Dahinden P, Dimroth P (2002) Subunit gamma of the oxaloacetate decarboxylase Na(+) pump: interaction with other subunits/ domains of the complex and binding site for the Zn(2+) metal ion. Biochemistry 41: 1285-1292.
14. Demchenko AP (1982) On the nanosecond mobility in proteins. Edge excitation fluorescence red shift of protein-bound 2-(p-toluidinylnaphthalene)-6-sulfonate. Biophys Chem 15: 101-109.
15. Lakowicz JR, Keating-Nakamoto S (1984) Red-edge excitation of fluorescence and dynamic properties of proteins and membranes. Biochemistry 23: 3013-3021.
16. Chattopadhyay A, Rukmini R (1993) Restricted mobility of the sole tryptophan in membrane-bound melittin. FEBS Lett 335: 341-344.
17. Surewicz WK, Mantsch HH (1988) New insight into protein secondary structure from resolution-enhanced infrared spectra. Biochim Biophys Acta 952: 115-130.
18. Surewicz WK, Mantsch HH, Chapman D (1993) Determination of protein secondary structure by Fourier transform infrared spectroscopy: a critical assessment. Biochemistry 32: 389-394.
19. Byler MD, Susi H (1986) Examination of the secondary structure of proteins by deconvolved FTIR spectra. Biopolymers 25: 469-487.
20. Susi H (1972) Infrared spectroscopy-conformation. Methods Enzymol 26 PtC: 455-472.
21. Birks JB (1970) Photophysics of Aromatic Molecules. London: Wiley-Interscience. 704 p.
22. Demchenko AP (2002) The red-edge effects: 30 years of exploration. Luminescence 17: 19-42.
23. Demchenko AP (1988) Red-edge-excitation fluorescence spectroscopy of singletryptophan proteins. Eur Biophys J 16: 121-129.
24. Mukherjee S, Chattopadhyay A (1994) Motionally restricted tryptophan environments at the peptide-lipid interface of gramicidin channels. Biochemistry 33: 5089-5097.
25. Granjon T, Vacheron MJ, Vial C, Buchet R (2001) Mitochondrial creatine kinase binding to phospholipids decreases fluidity of membranes and promotes new lipid-induced beta structures as monitored by red edge excitation shift, laurdan fluorescence, and FTIR. Biochemistry 40: 6016-6026.
26. Chattopadhyay A (2003) Exploring membrane organization and dynamics by the wavelength-selective fluorescence approach. Chem Phys Lipids 122: 3-17.
27. Rawat SS, Kelkar DA, Chattopadhyay A (2004) Monitoring gramicidin conformations in membranes: a fluorescence approach. Biophys J 87: 831-843.
28. Goormaghtigh E, Cabiaux V, Ruysschaert JM (1994) Determination of soluble and membrane protein structure by Fourier transform infrared spectroscopy 1.Assignments and Models compounds in Subcellular Biochemistry. New York: Plenum Press. pp 329-362.
29. Jackson M, Mantsch HH (1995) The use and misuse of FTIR spectroscopy in the determination of protein structure. Crit Rev Biochem Mol Biol 30: 95-120.
30. Cladera J, Sabes M, Padros E (1992) Fourier transform infrared analysis of bacteriorhodopsin secondary structure. Biochemistry 31: 12363-12368.
31. Torres J, Padros E (1995) Spectroscopic studies of bacteriorhodopsin fragments dissolved in organic solution. Biophys J 68: 2049-2055.
32. Tatulian SA, Biltonen RL, Tamm LK (1997) Structural changes in a secretory phospholipase A2 induced by membrane binding: a clue to interfacial activation? J Mol Biol 268: 809-815.
33. Fabian H, Naumann D, Misselwitz R, Ristau O, Gerlach D, et al. (1992) Secondary structure of streptokinase in aqueous solution: a Fourier transform infrared spectroscopic study. Biochemistry 31: 6532-6538.
34. Arrondo JL, Muga A, Castresana J, Goni FM (1993) Quantitative studies of the structure of proteins in solution by Fourier-transform infrared spectroscopy. Prog Biophys Mol Biol 59: 23-56.
35. Jockel P, Di Berardino M, Dimroth P (1999) Membrane topology of the betasubunit of the oxaloacetate decarboxylase Na+ pump from Klebsiella pneumoniae. Biochemistry 38: 13461-13472.
36. Barth A (2000) The infrared absorption of amino acid side chains. Prog Biophys Mol Biol 74: 141-173.
37. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, et al. (1999) Short protocols in molecular biology. New York: John Wiley & Sons. 1200 p.
38. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual; Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory. 1659 p.
39. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chainterminating inhibitors. Proc Natl Acad Sci U S A 74: 5463-5467.
40. Miroux B, Walker JE (1996) Over-production of proteins in Escherichia coli: mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels. J Mol Biol 260: 289-298.
41. Dahinden P, Pos KM, Taralczak M, Dimroth P (2004) Oxaloacetate decarboxylase of Archaeoglobus fulgidus: cloning of genes and expression in Escherichia coli. Arch Microbiol 182: 414-420.
42. Dahinden P, Auchli Y, Granjon T, Taralczak M, Wild M, et al. (2005) Oxaloacetate decarboxylase of Vibrio cholerae: purification, characterization, and expression of the genes in Escherichia coli. Arch Microbiol 183: 121-129.
43. Dimroth P, Thomer A (1986) Kinetic analysis of the reaction mechanism of oxaloacetate decarboxylase from Klebsiella aerogenes. Eur J Biochem 156: 157-162.
44. Glasoe PK, Long FA (1960) Use of glass electrodes to measure acidities in deuterium oxide. J Physiol Chem 64: 188-190.