Biochemical characterization of isocitrate dehydrogenase from Methylococcus capsulatus reveals a unique NAD+-dependent homotetrameric enzyme

Archives of Microbiology

Volumn 187, Issue 5, 2007, Pages 361-370

  Stokke, Runar ^a   Madern, Dominique ^b   Fedøy, Anita Elin ^a   Karlsen, Solveig ^c   Birkeland, Nils Kåre ^a   Steen, Ida Helene ^a  

^a UNIVERSITY OF BERGEN   (Norway)

^b INSTITUT DE BIOLOGIE STRUCTURALE   (France)

^c UNIVERSITY OF TROMSØ   (Norway)

Author keywords

Decarboxylating dehydrogenase; Cofactor specificity; Homoisocitrate dehydrogenase; Isocitrate dehydrogenase; Isopropylmalate dehydrogenase; Methylococcus capsulatus; Tetrameric

Indexed keywords

BACTERIAL ENZYME; HOMODIMER; ISOCITRATE DEHYDROGENASE (NAD); TETRAMER;

ALLOSTERISM; AMINO ACID SEQUENCE; ARTICLE; ENZYME ACTIVITY; ENZYME PURIFICATION; ENZYME STRUCTURE; ESCHERICHIA COLI; GENE OVEREXPRESSION; METHYLOCOCCUS CAPSULATUS; MITOCHONDRIAL GENE; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; TEMPERATURE DEPENDENCE; THERMAL ANALYSIS; THERMUS THERMOPHILUS; ULTRACENTRIFUGATION;

ALCOHOL OXIDOREDUCTASES; ISOCITRATE DEHYDROGENASE; METHYLOCOCCUS CAPSULATUS; NAD; PHYLOGENY; SUBSTRATE SPECIFICITY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; EUKARYOTA; METHYLOCOCCUS CAPSULATUS; THERMUS THERMOPHILUS;

EID: 34247097911     PISSN: 03028933     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00203-006-0200-y     Document Type: Article

References (45)

1. Aoshima M, Oshima T (1997) Purification and characterization of isocitrate dehydrogenase from a hyperthermophilic archaebacterium, Caldococcus noboribetus. Biochim Biophys Acta 1340:227-234
2. Bradford MM (1976) A rapid and sensitive method for the quantification of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 7:248-254
3. Camacho ML, Brown RA, Bonete MJ, Danson MJ, Hough DW (1995) Isocitrate dehydrogenases from Haloferax volcanii and Sulfolobus solfataricus - enzyme-purification, characterization and N-terminal sequence. FEMS Microbiol Lett 134:85-90
4. 2+ and isocitrate-insights into the enzyme mechanism. J Biol Chem 277:43454-43462
5. Chen RD, Greer A, Dean AM (1995) A highly active decarboxylating dehydrogenase with rationally inverted coenzyme speciWcity. Proc Natl Acad Sci USA 92:11666-11670
6. Chen RD, Greer A, Dean AM (1996) Redesigning secondary structure to invert coenzyme specificity in isopropylmalate dehydrogenase. Proc Natl Acad Sci USA 93:12171-12176
7. Chen RD, Greer AF, Dean AM (1997) Structural constraints in protein engineering-the coenzyme specificity of Escherichia coli isocitrate dehydrogenase. Eur J Biochem 250:578-582
8. Chen RD, Jeong SS (2000) Functional prediction: identification of protein orthologs and paralogs. Protein Sci 9:2344-2353
9. Dean AM, Golding GB (1997) Protein engineering reveals ancient adaptive replacements in isocitrate dehydrogenase. Proc Natl Acad Sci USA 94:3104-3109
10. Eikmanns BJ, Rittmann D, Sahm H (1995) Cloning, sequence analysis, expression, and inactivation of the Corynebacterium glutamicum Icd gene encoding isocitrate dehydrogenase and biochemical characterization of the enzyme. J Bacteriol 177:774-782
11. Eisenthal R, Cornish-Bowden A (1974) Direct linear plot - new graphical procedure for estimating enzyme kinetic-parameters. Biochem J 139:715-720
12. +-specificity from Vibrio parahaemolyticus Y-4. J Biochem (Tokyo) 112:849-855
13. Galvez S, Gadal P (1995) On the function of the NADP-dependent isocitrate dehydrogenase isoenzymes in living organisms. Plant Sci 105:1-14
14. Gouet P, Courcelle E, Stuart DI, Metoz F (1999) ESPript: analysis of multiple sequence alignments in postscript. Bioinformatics 15:305-308
15. Gray MW, Doolittle WF (1982) Has the endosymbiont hypothesis been proven? Microbiol Rev 46:1-42
16. Hurley JH, Thorsness PE, Ramalingam V, Helmers NH, Koshland DE, Stroud RM (1989) Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase. Proc Natl Acad Sci USA 86:8635-8639
17. Imada K, Sato M, Tanaka N, Katsube Y, Matsuura Y, Oshima T (1991) 3-Dimensional structure of a highly thermostable enzyme, 3-isopropylmalate dehydrogenase of Thermus thermophilus at 2.2 Å resolution. J Mol Biol 222:725-738
18. Imada K, Inagaki K, Matsunami H, Kawaguchi H, Tanaka H, Tanaka N, Namba K (1998) Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 angstrom resolution: the role of Glu88 in the unique substrate-recognition mechanism. Structure 6:971-982
19. +-dependent isocitrate dehydrogenase from the chemolithotroph Acidithiobacillus thiooxidans. FEMS Microbiol Lett 214:127-132
20. Kanao T, Kawamura M, Fukui T, Atomi H, Imanaka T (2002) Characterization of isocitrate dehydrogenase from the green sulfur bacterium Chlorobium limicola - a carbon dioxide-Wxing enzyme in the reductive tricarboxylic acid cycle. Eur J Biochem 269:1926-1931
21. Karlström M, Stokke R, Steen IH, Birkeland NK, Ladenstein R (2005) Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix: X-ray structure analysis of a ternary enzyme-substrate complex and thermal stability. J Mol Biol 345:559-577
22. Karlström M, Steen IH, Madern D, Fedøy AE, Birkeland NK, Ladenstein R (2006) The crystal structure of a hyperthermostable subfamily II isocitrate dehydrogenase from Thermotoga maritima. Febs J 273:2851-2868
23. Lancien M, Gadal P, Hodges M (1998) Molecular characterization of higher plant NAD-dependent isocitrate dehydrogenase: evidence for a heteromeric structure by the complementation of yeast mutants. Plant J 16:325-333
24. Lloyd AJ, Weitzman PDJ (1988) Purification and characterization of NAD-linked isocitrate dehydrogenase from Methylophilus methylotrophus. Biochem Soc Trans 16:871-872
25. Maki S, Yoneta M, Takada Y (2006) Two isocitrate dehydrogenases from a psychrophilic bacterium, Colwellia psychrerythraea. Extremophiles 10:237-249
26. Miyazaki J, Asada K, Fushinobu S, Kuzuyama T, Nishiyama M (2005) Crystal structure of tetrameric homoisocitrate dehydrogenase from an extreme thermophile, Thermus thermophilus: involvement of hydrophobic dimer-dimer interaction in extremely high thermotolerance. J Bacteriol 187:6779-6788
27. Miyazaki K, Kakinuma K, Terasawa H, Oshima T (1993) Kineticanalysis on the substrate-specificity of 3-isopropylmalate dehydrogenase. FEBS Lett 332:35-36
28. Miyazaki K (1996) Isocitrate dehydrogenase from Thermus aquaticus YT1: Purification of the enzyme and cloning, sequencing, and expression of the gene. Appl Environ Microbiol 62:4627-4631
29. Miyazaki K (2005a) Bifunctional isocitrate-homoisocitrate dehydrogenase: a missing link in the evolution of beta-decarboxylating dehydrogenase. Biochem Biophys Res Commun 331:341-346
30. Miyazaki K (2005b) Identification of a novel trifunctional homoisocitrate dehydrogenase and modulation of the broad substrate specificity through site-directed mutagenesis. Biochem Biophys Res Commun 336:596-602
31. +-isocitrate dehydrogenase from the cyanobacterium Anabaena sp. strain PCC 7120: purification and characterization of the enzyme and cloning, sequencing, and disruption of the Icd Gene. J Bacteriol 176:2718-2726
32. Schuck P (2000) Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and Lamm equation modeling. Biophys J 78:1606-1619
33. Singh SK, Miller SP, Matsuno K, Sonenshein AL, LaPorte DC, Banaszak LJ (1999) Crystal structure of isocitrate dehydrogenase from B. subtilis. FASEB J 13:A1560-A1560
34. Singh SK, Miller SP, Dean A, Banaszak LJ, LaPorte DC (2002) Bacillus subtilis isocitrate dehydrogenase - a substrate analogue for Escherichia coli isocitrate dehydrogenase kinase/ phosphatase. J Biol Chem 277:7567-7573
35. Steen IH, Madsen MS, Birkeland NK, Lien T (1998) Purification and characterization of a monomeric isocitrate dehydrogenase from the sulfate-reducing bacterium Desulfobacter vibrioformis and demonstration of the presence of a monomeric enzyme in other bacteria. FEMS Microbiol Lett 160:75-79
36. Steen IH, Madern D, Karlström M, Lien T, Ladenstein R, Birkeland NK (2001) Comparison of isocitrate dehydrogenase from three hyperthermophiles reveals differences in thermostability, cofactor specificity, oligomeric state, and phylogenetic aYliation. J Biol Chem 276:43924-43931
37. Suzuki T, Inoki Y, Yamagishi A, Iwasaki T, Wakagi T, Oshima T (1997) Molecular and phylogenetic characterization of isopropylmalate dehydrogenase of a thermoacidophilic archaeon, Sulfolobus sp. strain 7. J Bacteriol 179:1174-1179
38. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: Xexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882
39. Timmis JN, Ayliffe MA, Huang CY, Martin W (2004) Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 5:123-135
40. Tipton PA, Beecher BS (1994) Tartrate dehydrogenase, a new member of the family of metal-dependent decarboxylating R-hydroxyacid dehydrogenases. Arch Biochem Biophys 313:15-21
41. Vieille C, Zeikus GJ (2001) Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol Mol Biol Rev 65:1-43
42. Wallon G, Kryger G, Lovett ST, Oshima T, Ringe D, Petsko GA (1997) Crystal structures of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus. J Mol Biol 266:1016-1031
43. Ward N, Larsen O, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang LX, Scanlan D, Kang KH, Lewis M, Nelson KE, Methe B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren QH, Read T, DeBoy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, Eisen JA (2004) Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). Plos Biol 2:1616-1628
44. Xu X, Zhao JY, Xu Z, Peng BZ, Huang QH, Arnold E, Ding JP (2004) Structures of human cytosolic NADP-dependent isocitrate dehydrogenase reveal a novel self-regulatory mechanism of activity. J Biol Chem 279:33946-33957
45. Zhang T, Koshland DE (1995) Modeling substrate binding in Thermus thermophilus isopropylmalate dehydrogenase. Protein Sci 4:84-92