Crystal structure of the Pyrococcus horikoshii isopropylmalate isomerase small subunit provides insight into the dual substrate specificity of the enzyme

Journal of Molecular Biology

Volumn 344, Issue 2, 2004, Pages 325-333

  Yasutake, Yoshiaki ^a   Yao, Min ^a   Sakai, Naoki ^a   Kirita, Tomomi ^a   Tanaka, Isao ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

Author keywords

aconitase; crystal structure; homoaconitase; isopropylmalate isomerase; Pyrococcus horikoshii

Indexed keywords

ACONITATE HYDRATASE; BACTERIAL ENZYME; HOMOCITRATE; ISOENZYME; ISOPROPYLMALATE ISOMERASE; MONOMER; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; CRYSTAL STRUCTURE; DISULFIDE BOND; ENZYME SPECIFICITY; ENZYME SUBUNIT; HIGH TEMPERATURE; HYDROPHILICITY; HYDROPHOBICITY; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PYROCOCCUS; PYROCOCCUS HORIKOSHII; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS;

ARCHAEA; PYROCOCCUS; PYROCOCCUS HORIKOSHII;

EID: 7444246744     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.09.035     Document Type: Article

References (47)

1. S.R. Gross, R.O. Burns, and H.E. Umbarger The biosynthesis of leucine. II: the enzymic isomerization of β-carboxy-β-hydroxyisocaproate and α-hydroxy-β-carboxyisocaproate Biochemistry 2 1963 1046 1052
2. P. Margolin Genetic fine structure of the leucine operon in Salmonella Genetics 48 1963 441 457
3. J.J. Ward, and S.A. Zahler Genetic studies of leucine biosynthesis in Bacillus subtilis J. Bacteriol. 116 1973 719 726
4. J.J. Godon, M.C. Chopin, and S.D. Ehrlich Branched-chain amino acid biosynthesis genes in Lactococcus lactis subsp. lactis J. Bacteriol. 174 1992 6580 6589
5. M. Tamakoshi, A. Yamagishi, and T. Oshima The organization of the leuC, leuD and leuB genes of extreme thermophile Thermus thermophilus Gene 222 1998 125 132
6. M.J. Gruer, P.J. Artymiuk, and J.R. Guest The aconitase family: three structural variations on a common theme Trends Biochem. Sci. 22 1997 3 6
7. A.H. Robbins, and C.D. Stout Structure of activated aconitase: formation of the [4Fe-4S] cluster in the crystal Proc. Natl Acad. Sci. USA 86 1989 3639 3643
8. H. Lauble, M.C. Kennedy, H. Beinert, and C.D. Stout Crystal structures of aconitase with isocitrate and nitroisocitrate bound Biochemistry 31 1992 2735 2748
9. H. Lauble, M.C. Kennedy, H. Beinert, and C.D. Stout Crystal structures of aconitase with trans-aconitate and nitrocitrate bound J. Mol. Biol. 237 1994 437 451
10. H. Lauble, and C.D. Stout Steric and conformational features of the aconitase mechanism Proteins: Struct. Funct. Genet. 22 1995 1 11
11. H. Lauble, M.C. Kennedy, M.H. Emptage, H. Beinert, and C.D. Stout The reaction of fluorocitrate with aconitase and the crystal structure of the enzyme-inhibitor complex Proc. Natl Acad. Sci. USA 93 1996 13699 13703
12. S.J. Lloyd, H. Lauble, G.S. Prasad, and C.D. Stout The mechanism of aconitase: 1.8 Å crystal structure of the S642A:citrate complex Protein Sci. 8 1999 2655 2662
13. C.H. Williams, T.J. Stillman, V.V. Barynin, S.E. Sedelnikova, Y. Tang, and J. Green E. coli aconitase B structure reveals a heat-like domain with implications for protein protein recognition Nature Struct. Biol. 9 2002 447 452
14. P.N. Fultz, and J. Kemper Wild-type isopropylmalate isomerase in Salmonella typhimurium is composed of two different subunits J. Bacteriol. 148 1981 210 219
15. H. Nishida, M. Nishiyama, N. Kobashi, T. Kosuge, T. Hoshino, and H. Yamane A prokaryotic gene cluster involved in synthesis of lysine through the amino adipate pathway: a key to the evolution of amino acid biosynthesis Genome Res. 9 1999 1175 1183
16. T. Lombo, N. Takaya, J. Miyazaki, K. Gotoh, M. Nishiyama, and T. Kosuge Functional analysis of the small subunit of the putative homoaconitase from Pyrococcus horikoshii in the Thermus lysine biosynthetic pathway FEMS Microbiol. Letters 233 2004 315 324
17. B.W. Matthews Solvent content of protein crystals J. Mol. Biol. 33 1968 491 497
18. K. Ogasahara, N.N. Khechinashvili, M. Nakamura, T. Yoshimoto, and K. Yutani Thermal stability of pyrrolidone carboxyl peptidases from the hyperthermophilic archaeon, Pyrococcus furiosus Eur. J. Biochem. 268 2001 3233 3242
19. Y. Tanaka, K. Tsumoto, Y. Yasutake, M. Umetsu, M. Yao, and H. Fukada How oligomerization contributes to the thermostability of an archaeon protein: protein l-isoaspartyl-O-methyltransferase from Sulfolobus tokodaii J. Biol. Chem. 279 2004 32957 32967
20. T. Kabashima, Y. Li, N. Kanada, K. Ito, and T. Yoshimoto Enhancement of the thermal stability of pyroglutamyl peptidase I by introduction of an intersubunit disulfide bond Biochim. Biophys. Acta 1547 2001 214 220
21. L. Holm, and C. Sander Protein structure comparison by alignment of distance matrices J. Mol. Biol. 233 1993 123 138
22. S.D. Irvin, and J.K. Bhattacharjee A unique fungal lysine biosynthesis enzyme shares a common ancestor with tricarboxylic acid cycle and leucine biosynthetic enzymes found in diverse organisms J. Mol. Evol. 46 1998 401 408
23. G. Weidner, B. Steffan, and A.A. Brakhage The Aspergillus nidulans lysF gene encodes homoaconitase, an enzyme involved in the fungus-specific lysine biosynthesis pathway Mol. Gen. Genet. 255 1997 237 247
24. T. Kosuge, and T. Hoshino Lysine is synthesized through the α-aminoadipate pathway in Thermus thermophilus FEMS Microbiol. Letters 15 1998 361 367
25. N. Kobashi, M. Nishiyama, and M. Tanokura Aspartate kinase-independent lysine synthesis in an extremely thermophilic bacterium, Thermus thermophilus: lysine is synthesized via α-aminoadipic acid not via diaminopimelic acid J. Bacteriol. 181 1999 1713 1718
26. M.W. Hentze, and L.C. Kuhn Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress Proc. Natl Acad. Sci. USA 93 1996 8175 8182
27. E.G. Meyron-Holtz, M.C. Ghosh, K. Iwai, T. LaVaute, X. Brazzolotto, and U.V. Berger Genetic ablations of iron regulatory proteins 1 and 2 reveal why iron regulatory protein 2 dominates iron homeostasis EMBO J. 23 2004 386 395
28. J. Miyazaki, N. Kobashi, M. Nishiyama, and H. Yamane Characterization of homoisocitrate dehydrogenase involved in lysine biosynthesis of an extremely thermophilic bacterium, Thermus thermophilus HB27, and evolutionry implication of β-decarboxylating dehydrogenase J. Biol. Chem. 278 2003 1864 1872
29. M.W. Bauer, E.J. Bylina, R.V. Swanson, and R.M. Kelly Comparison of a β-glucosidase and a β-mannosidase from the hyperthermophilic archaeon Pyrococcus furiosus: purification, characterization, gene cloning, and sequence analysis J. Biol. Chem. 271 1996 23749 23755
30. V. Durbecq, C. Legrain, M. Roovers, A. Pierard, and N. Glansdorff The carbamate kinase-like carbamoyl phosphate synthetase of the hyperthermophilic archaeon Pyrococcus furiosus, a missing link in the evolution of carbamoyl phosphate biosynthesis Proc. Natl Acad. Sci. USA 94 1997 12803 12808
31. I. Matsui, E. Matsui, Y. Sakai, H. Kikuchi, Y. Kawarabayasi, and H. Ura The molecular structure of hyperthermostable aromatic aminotransferase with novel substrate specificity from Pyrococcus horikoshii J. Biol. Chem. 275 2000 4871 4879
32. K. Ishikawa, H. Ishida, I. Matsui, Y. Kawarabayashi, and H. Kikuchi Novel bifunctional hyperthermostable carboxypeptidase/aminoacylase from Pyrococcus horikoshii OT3 Appl. Environ. Microbiol. 67 2001 673 679
33. W. Kabsch A solution for the best rotation to relate two sets of vectors Acta Crystallog. sect. A 32 1976 922 923
34. P.J. Kraulis MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallog. 24 1991 946 950
35. E.A. Merritt, and D.J. Bacon Raster3D: photorealistic graphics Methods Enzymol. 277 1997 505 524
36. J.D. Thompson, D.G. Higgins, and T.J. Gibson 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
37. J.M. Harp, D.E. Timm, and G.J. Bunick Macromolecular crystal annealing: overcoming increased mosaicity associated with cryocrystallography Acta Crystallog. sect. D 54 1998 622 628
38. A.G.W. Leslie Auto-indexing of rotation diffraction images and parameter refinement L. Sawyer N. Isaacs S. Bailey Proceeding of the CCP4 Study Weekend 1993 Daresbury Laboratory Warrington, UK 44 51
39. Collaborative Computational Project, Number 4 Acta Crystallog. sect. D 50 1994 760 763
40. T.C. Terwilliger, and J. Berendzen Automated MAD and MIR structure solution Acta Crystallog. sect. D 55 1999 849 861
41. E. de la Fortelle, and G. Bricogne Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods Methods Enzymol. 276 1997 472 494
42. J.P. Abrahams, and A.G.W. Leslie Methods used in the structure determination of bovine mitochondrial F1 ATPase Acta Crystallog. sect. D 52 1996 30 42
43. J. Navaza AMoRe: an automated package for molecular replacement Acta Crystallog. sect. D 50 1994 157 163
44. A. Perrakis, R. Morris, and V.S. Lamzin Automated-protein model building combined with iterative structure refinement Nature Struct. Biol. 6 1999 458 463
45. T.A. Jones, J.Y. Zou, S.W. Cowan, and M. Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallog. sect. A 47 1991 110 119
46. A.T. Brünger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, and R.W. Grosse-Kunstleve Crystallography and NMR system (CNS): a new software suite for macromolecular structure determination Acta crystallog. sect. D 54 1998 905 921
47. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallog. 26 1993 283 291