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Triose-phosphate isomerase (TIM) of the psychrophilic bacterium Vibrio marinus. Kinetic and structural properties.

Alvarez M, Zeelen JP, Mainfroid V, Rentier-Delrue F, Martial JA, Wyns L, Wierenga RK, Maes D
J Biol Chem 273 2199-206 (1998)
Cited: 79 times
EuropePMC logo PMID: 9442062

Abstract

The purification and characterization of triose-phosphate isomerase from the psychrophilic bacterium Vibrio marinus (vTIM) is described. Crystal structures of the vTIM-sulfate complex and the vTIM-2-phosphoglycolate complex (at a 2.7-A resolution) are also presented. The optimal growth temperature of Vibrio marinus is 15 degrees C. Stability studies show that vTIM is an unstable protein with a half-life of only 10 min at 25 degrees C. The vTIM sequence is most closely related to the sequence of Escherichia coli TIM (eTIM) (66% identity), and several unique structural features described for eTIM are also seen in vTIM, but eTIM is considerably more stable. The Td values of vTIM and eTIM, determined by calorimetric studies, are 41 and 54 degrees C, respectively. Amino acid sequence comparison reveals that vTIM has an alanine in loop 8 (at position 238), whereas all other TIM sequences known to date have a serine. The vTIM mutant A238S was produced and characterized. Compared with wild type, the catalytic efficiency of the A238S mutant is somewhat reduced, and its stability is considerably increased.

Reviews - 1aw2 mentioned but not cited (1)

  1. Discovery, Molecular Mechanisms, and Industrial Applications of Cold-Active Enzymes. Santiago M, Ramírez-Sarmiento CA, Zamora RA, Parra LP. Front Microbiol 7 1408 (2016)

Articles - 1aw2 mentioned but not cited (2)

  1. Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding. Li Z, He Y, Liu Q, Zhao L, Wong L, Kwoh CK, Nguyen H, Li J. BMC Bioinformatics 14 Suppl 16 S11 (2013)
  2. Crystallographically correct but confusing presentation of structural models deposited in the Protein Data Bank. Dauter Z, Wlodawer A. Acta Crystallogr D Struct Biol 74 939-945 (2018)


Reviews citing this publication (10)

  1. The stability of proteins in extreme environments. Jaenicke R, Böhm G. Curr Opin Struct Biol 8 738-748 (1998)
  2. Cold-adapted enzymes. Siddiqui KS, Cavicchioli R. Annu Rev Biochem 75 403-433 (2006)
  3. Cold-adapted enzymes: from fundamentals to biotechnology. Gerday C, Aittaleb M, Bentahir M, Chessa JP, Claverie P, Collins T, D'Amico S, Dumont J, Garsoux G, Georlette D, Hoyoux A, Lonhienne T, Meuwis MA, Feller G. Trends Biotechnol 18 103-107 (2000)
  4. Low-temperature extremophiles and their applications. Cavicchioli R, Siddiqui KS, Andrews D, Sowers KR. Curr Opin Biotechnol 13 253-261 (2002)
  5. Molecular basis of cold adaptation. D'Amico S, Claverie P, Collins T, Georlette D, Gratia E, Hoyoux A, Meuwis MA, Feller G, Gerday C. Philos Trans R Soc Lond B Biol Sci 357 917-925 (2002)
  6. Psychrophilic enzymes: from folding to function and biotechnology. Feller G. Scientifica (Cairo) 2013 512840 (2013)
  7. Optimization to low temperature activity in psychrophilic enzymes. Struvay C, Feller G. Int J Mol Sci 13 11643-11665 (2012)
  8. A guide to the effects of a large portion of the residues of triosephosphate isomerase on catalysis, stability, druggability, and human disease. Olivares-Illana V, Riveros-Rosas H, Cabrera N, Tuena de Gómez-Puyou M, Pérez-Montfort R, Costas M, Gómez-Puyou A. Proteins 85 1190-1211 (2017)
  9. Multifactorial level of extremostability of proteins: can they be exploited for protein engineering? Chakravorty D, Khan MF, Patra S. Extremophiles 21 419-444 (2017)
  10. Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes. Cifuente JO, Colleoni C, Kalscheuer R, Guerin ME. Chem Rev 124 4863-4934 (2024)

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  1. Tandem repeats in proteins: from sequence to structure. Kajava AV. J Struct Biol 179 279-288 (2012)
  2. Structures of the psychrophilic Alteromonas haloplanctis alpha-amylase give insights into cold adaptation at a molecular level. Aghajari N, Feller G, Gerday C, Haser R. Structure 6 1503-1516 (1998)
  3. Tiny TIM: a small, tetrameric, hyperthermostable triosephosphate isomerase. Walden H, Bell GS, Russell RJ, Siebers B, Hensel R, Taylor GL. J Mol Biol 306 745-757 (2001)
  4. Function and biotechnology of extremophilic enzymes in low water activity. Karan R, Capes MD, Dassarma S. Aquat Biosyst 8 4 (2012)
  5. Comparative structural analysis of psychrophilic and meso- and thermophilic enzymes. Gianese G, Bossa F, Pascarella S. Proteins 47 236-249 (2002)
  6. The crystal structure of triosephosphate isomerase (TIM) from Thermotoga maritima: a comparative thermostability structural analysis of ten different TIM structures. Maes D, Zeelen JP, Thanki N, Beaucamp N, Alvarez M, Thi MH, Backmann J, Martial JA, Wyns L, Jaenicke R, Wierenga RK. Proteins 37 441-453 (1999)
  7. Comparative proteome analysis of psychrophilic versus mesophilic bacterial species: Insights into the molecular basis of cold adaptation of proteins. Metpally RP, Reddy BV. BMC Genomics 10 11 (2009)
  8. Structural and mutagenesis studies of leishmania triosephosphate isomerase: a point mutation can convert a mesophilic enzyme into a superstable enzyme without losing catalytic power. Williams JC, Zeelen JP, Neubauer G, Vriend G, Backmann J, Michels PA, Lambeir AM, Wierenga RK. Protein Eng 12 243-250 (1999)
  9. Structural adaptation of enzymes to low temperatures. Gianese G, Argos P, Pascarella S. Protein Eng 14 141-148 (2001)
  10. Crystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases. Aghajari N, Van Petegem F, Villeret V, Chessa JP, Gerday C, Haser R, Van Beeumen J. Proteins 50 636-647 (2003)
  11. Temperature adaptation of proteins: engineering mesophilic-like activity and stability in a cold-adapted alpha-amylase. D'Amico S, Gerday C, Feller G. J Mol Biol 332 981-988 (2003)
  12. Structural comparison of psychrophilic and mesophilic trypsins. Elucidating the molecular basis of cold-adaptation. Leiros HK, Willassen NP, Smalås AO. Eur J Biochem 267 1039-1049 (2000)
  13. Structure of a full length psychrophilic cellulase from Pseudoalteromonas haloplanktis revealed by X-ray diffraction and small angle X-ray scattering. Violot S, Aghajari N, Czjzek M, Feller G, Sonan GK, Gouet P, Gerday C, Haser R, Receveur-Bréchot V. J Mol Biol 348 1211-1224 (2005)
  14. The 1.9 A crystal structure of heat-labile shrimp alkaline phosphatase. de Backer M, McSweeney S, Rasmussen HB, Riise BW, Lindley P, Hough E. J Mol Biol 318 1265-1274 (2002)
  15. Alkaline phosphatase from the Antarctic strain TAB5. Properties and psychrophilic adaptations. Rina M, Pozidis C, Mavromatis K, Tzanodaskalaki M, Kokkinidis M, Bouriotis V. Eur J Biochem 267 1230-1238 (2000)
  16. Cold-active beta-galactosidase from Arthrobacter sp. C2-2 forms compact 660 kDa hexamers: crystal structure at 1.9A resolution. Skálová T, Dohnálek J, Spiwok V, Lipovová P, Vondrácková E, Petroková H, Dusková J, Strnad H, Králová B, Hasek J. J Mol Biol 353 282-294 (2005)
  17. Differences in the intersubunit contacts in triosephosphate isomerase from two closely related pathogenic trypanosomes. Maldonado E, Soriano-García M, Moreno A, Cabrera N, Garza-Ramos G, de Gómez-Puyou M, Gómez-Puyou A, Perez-Montfort R. J Mol Biol 283 193-203 (1998)
  18. Crystal structure of a subtilisin-like serine proteinase from a psychrotrophic Vibrio species reveals structural aspects of cold adaptation. Arnórsdóttir J, Kristjánsson MM, Ficner R. FEBS J 272 832-845 (2005)
  19. Biotechnology of cold-active proteases. Joshi S, Satyanarayana T. Biology (Basel) 2 755-783 (2013)
  20. A DNA ligase from the psychrophile Pseudoalteromonas haloplanktis gives insights into the adaptation of proteins to low temperatures. Georlette D, Jónsson ZO, Van Petegem F, Chessa J, Van Beeumen J, Hübscher U, Gerday C. Eur J Biochem 267 3502-3512 (2000)
  21. Characterization of a cloned subtilisin-like serine proteinase from a psychrotrophic Vibrio species. Arnórsdottir J, Smáradóttir RB, Magnússon OT, Thorbjarnardóttir SH, Eggertsson G, Kristjánsson MM. Eur J Biochem 269 5536-5546 (2002)
  22. Properties of a subtilisin-like proteinase from a psychrotrophic Vibrio species comparison with proteinase K and aqualysin I. Kristjánsson MM, Magnússon OT, Gudmundsson HM, Alfredsson GA, Matsuzawa H. Eur J Biochem 260 752-760 (1999)
  23. Archaeal cold-adapted proteins: structural and evolutionary analysis of the elongation factor 2 proteins from psychrophilic, mesophilic and thermophilic methanogens. Thomas T, Cavicchioli R. FEBS Lett 439 281-286 (1998)
  24. Extreme catalysts from low-temperature environments. Hoyoux A, Blaise V, Collins T, D'Amico S, Gratia E, Huston AL, Marx JC, Sonan G, Zeng Y, Feller G, Gerday C. J Biosci Bioeng 98 317-330 (2004)
  25. Molecular analysis of the gene encoding a novel cold-adapted chitinase (ChiB) from a marine bacterium, Alteromonas sp. strain O-7. Orikoshi H, Baba N, Nakayama S, Kashu H, Miyamoto K, Yasuda M, Inamori Y, Tsujibo H. J Bacteriol 185 1153-1160 (2003)
  26. Metabolic enzymes from psychrophilic bacteria: challenge of adaptation to low temperatures in ornithine carbamoyltransferase from Moritella abyssi. Xu Y, Feller G, Gerday C, Glansdorff N. J Bacteriol 185 2161-2168 (2003)
  27. Closed conformation of the active site loop of rabbit muscle triosephosphate isomerase in the absence of substrate: evidence of conformational heterogeneity. Aparicio R, Ferreira ST, Polikarpov I. J Mol Biol 334 1023-1041 (2003)
  28. qPIPSA: relating enzymatic kinetic parameters and interaction fields. Gabdoulline RR, Gabdoulline RR, Stein M, Wade RC. BMC Bioinformatics 8 373 (2007)
  29. Structural adaptation to low temperatures--analysis of the subunit interface of oligomeric psychrophilic enzymes. Tronelli D, Maugini E, Bossa F, Pascarella S. FEBS J 274 4595-4608 (2007)
  30. Thermodynamic characterization of yeast triosephosphate isomerase refolding: insights into the interplay between function and stability as reasons for the oligomeric nature of the enzyme. Nájera H, Costas M, Fernández-Velasco DA. Biochem J 370 785-792 (2003)
  31. Cold-adapted alanine dehydrogenases from two antarctic bacterial strains: gene cloning, protein characterization, and comparison with mesophilic and thermophilic counterparts. Galkin A, Kulakova L, Ashida H, Sawa Y, Esaki N. Appl Environ Microbiol 65 4014-4020 (1999)
  32. Crystal structure of alkaline phosphatase from the Antarctic bacterium TAB5. Wang E, Koutsioulis D, Leiros HK, Andersen OA, Bouriotis V, Hough E, Heikinheimo P. J Mol Biol 366 1318-1331 (2007)
  33. Exploring the role of a glycine cluster in cold adaptation of an alkaline phosphatase. Mavromatis K, Tsigos I, Tzanodaskalaki M, Kokkinidis M, Bouriotis V. Eur J Biochem 269 2330-2335 (2002)
  34. Susceptibility to proteolysis of triosephosphate isomerase from two pathogenic parasites: characterization of an enzyme with an intact and a nicked monomer. Reyes-Vivas H, Martínez-Martínez E, Mendoza-Hernández G, López-Velázquez G, Pérez-Montfort R, Tuena de Gómez-Puyou M, Gómez-Puyou A. Proteins 48 580-590 (2002)
  35. Unfolding of triosephosphate isomerase from Trypanosoma brucei: identification of intermediates and insight into the denaturation pathway using tryptophan mutants. Chánez-Cárdenas ME, Fernández-Velasco DA, Vázquez-Contreras E, Coria R, Saab-Rincón G, Pérez-Montfort R. Arch Biochem Biophys 399 117-129 (2002)
  36. Disulfide bridges in the mesophilic triosephosphate isomerase from Giardia lamblia are related to oligomerization and activity. Reyes-Vivas H, Diaz A, Peon J, Mendoza-Hernandez G, Hernandez-Alcantara G, De la Mora-De la Mora I, Enriquez-Flores S, Dominguez-Ramirez L, Lopez-Velazquez G. J Mol Biol 365 752-763 (2007)
  37. Modeling, mutagenesis, and structural studies on the fully conserved phosphate-binding loop (loop 8) of triosephosphate isomerase: toward a new substrate specificity. Norledge BV, Lambeir AM, Abagyan RA, Rottmann A, Fernandez AM, Filimonov VV, Peter MG, Wierenga RK. Proteins 42 383-389 (2001)
  38. Structure and function of a regulated archaeal triosephosphate isomerase adapted to high temperature. Walden H, Taylor GL, Lorentzen E, Pohl E, Lilie H, Schramm A, Knura T, Stubbe K, Tjaden B, Hensel R. J Mol Biol 342 861-875 (2004)
  39. Computer simulations explain the anomalous temperature optimum in a cold-adapted enzyme. Sočan J, Purg M, Åqvist J. Nat Commun 11 2644 (2020)
  40. Genomic analysis of cold-active Colwelliaphage 9A and psychrophilic phage-host interactions. Colangelo-Lillis JR, Deming JW. Extremophiles 17 99-114 (2013)
  41. Cold-active citrate synthase: mutagenesis of active-site residues. Gerike U, Danson MJ, Hough DW. Protein Eng 14 655-661 (2001)
  42. NADP+-dependent glutamate dehydrogenase in the Antarctic psychrotolerant bacterium Psychrobacter sp. TAD1. Characterization, protein and DNA sequence, and relationship to other glutamate dehydrogenases. Di Fraia R, Wilquet V, Ciardiello MA, Carratore V, Antignani A, Camardella L, Glansdorff N, Di Prisco G. Eur J Biochem 267 121-131 (2000)
  43. Psychrophily and catalysis. Gerday C. Biology (Basel) 2 719-741 (2013)
  44. ConSole: using modularity of contact maps to locate solenoid domains in protein structures. Hrabe T, Godzik A. BMC Bioinformatics 15 119 (2014)
  45. Cold-active enzymes studied by comparative molecular dynamics simulation. Spiwok V, Lipovová P, Skálová T, Dusková J, Dohnálek J, Hasek J, Russell NJ, Králová B. J Mol Model 13 485-497 (2007)
  46. Engineering the properties of a cold active enzyme through rational redesign of the active site. Tsigos I, Mavromatis K, Tzanodaskalaki M, Pozidis C, Kokkinidis M, Bouriotis V. Eur J Biochem 268 5074-5080 (2001)
  47. Characterization of photosynthetic ferredoxin from the Antarctic alga Chlamydomonas sp. UWO241 reveals novel features of cold adaptation. Cvetkovska M, Szyszka-Mroz B, Possmayer M, Pittock P, Lajoie G, Smith DR, Hüner NPA. New Phytol 219 588-604 (2018)
  48. Conformational selection in silico: loop latching motions and ligand binding in enzymes. Wong S, Jacobson MP. Proteins 71 153-164 (2008)
  49. Enhanced functionality and stabilization of a cold active laccase using nanotechnology based activation-immobilization. Mukhopadhyay A, Dasgupta AK, Chakrabarti K. Bioresour Technol 179 573-584 (2015)
  50. Engineering lipase A from mesophilic Bacillus subtilis for activity at low temperatures. Kumar V, Yedavalli P, Gupta V, Rao NM. Protein Eng Des Sel 27 73-82 (2014)
  51. Sequence and structural parameters enhancing adaptation of proteins to low temperatures. Jahandideh S, Abdolmaleki P, Jahandideh M, Barzegari Asadabadi E. J Theor Biol 246 159-166 (2007)
  52. Analysis of the psychrotolerant property of hormone-sensitive lipase through site-directed mutagenesis. Laurell H, Contreras JA, Castan I, Langin D, Holm C. Protein Eng 13 711-717 (2000)
  53. Reversibility and two state behaviour in the thermal unfolding of oligomeric TIM barrel proteins. Romero-Romero S, Costas M, Rodríguez-Romero A, Alejandro Fernández-Velasco D. Phys Chem Chem Phys 17 20699-20714 (2015)
  54. Lys13 plays a crucial role in the functional adaptation of the thermophilic triose-phosphate isomerase from Bacillus stearothermophilus to high temperatures. Alvarez M, Wouters J, Maes D, Mainfroid V, Rentier-Delrue F, Wyns L, Depiereux E, Martial JA. J Biol Chem 274 19181-19187 (1999)
  55. Biochemical and structural characterization of a novel cold-active esterase-like protein from the psychrophilic yeast Glaciozyma antarctica. Hashim NHF, Mahadi NM, Illias RM, Feroz SR, Abu Bakar FD, Murad AMA. Extremophiles 22 607-616 (2018)
  56. Structural and functional analysis of a novel psychrophilic β-mannanase from Glaciozyma antarctica PI12. Parvizpour S, Razmara J, Ramli AN, Md Illias R, Shamsir MS. J Comput Aided Mol Des 28 685-698 (2014)
  57. Molecular adaptation in the ice worm, Mesenchytraeus solifugus: divergence of energetic-associated genes. Farrell AH, Hohenstein KA, Shain DH. J Mol Evol 59 666-673 (2004)
  58. Structural insights from a novel invertebrate triosephosphate isomerase from Litopenaeus vannamei. Lopez-Zavala AA, Carrasco-Miranda JS, Ramirez-Aguirre CD, López-Hidalgo M, Benitez-Cardoza CG, Ochoa-Leyva A, Cardona-Felix CS, Diaz-Quezada C, Rudiño-Piñera E, Sotelo-Mundo RR, Brieba LG. Biochim Biophys Acta 1864 1696-1706 (2016)
  59. The Activation Parameters of a Cold-Adapted Short Chain Dehydrogenase Are Insensitive to Enzyme Oligomerization. Koenekoop L, van der Ent F, Purg M, Åqvist J. Biochemistry 61 514-522 (2022)
  60. Fungal Biomarkers Stability in Mars Regolith Analogues after Simulated Space and Mars-like Conditions. Cassaro A, Pacelli C, Baqué M, de Vera JP, Böttger U, Botta L, Saladino R, Rabbow E, Onofri S. J Fungi (Basel) 7 859 (2021)
  61. Cloning of triose phosphate isomerase gene from an antarctic psychrophilic Pseudomonas sp. by degenerate and splinkerette PCR. See Too WC, Few LL. World J Microbiol Biotechnol 26 1251-1259 (2010)
  62. Gene Cloning, Recombinant Expression, Characterization, and Molecular Modeling of the Glycolytic Enzyme Triosephosphate Isomerase from Fusarium oxysporum. Hernández-Ochoa B, Gómez-Manzo S, Alcaraz-Carmona E, Serrano-Posada H, Centeno-Leija S, Arreguin-Espinosa R, Cuevas-Cruz M, González-Valdez A, Mendoza-Espinoza JA, Acosta Ramos M, Cortés-Maldonado L, Montiel-González AM, Pérez de la Cruz V, Rocha-Ramírez LM, Marcial-Quino J, Sierra-Palacios E. Microorganisms 8 E40 (2019)
  63. Potential use of sugar binding proteins in reactors for regeneration of CO2 fixation acceptor D-Ribulose-1,5-bisphosphate. Mahato S, De D, Dutta D, Kundu M, Bhattacharya S, Schiavone MT, Bhattacharya SK. Microb Cell Fact 3 7 (2004)
  64. Cloning of glyceraldehyde-3-phosphate dehydrogenase from an Antarctic psychrophilic bacterium by inverse and splinkerette PCR. Too WC, Liew YC, Few LL. J Basic Microbiol 48 430-435 (2008)
  65. Conformational properties of striated muscle tropomyosins from some salmonid fishes. Goonasekara CL, Heeley DH. J Muscle Res Cell Motil 29 135-143 (2008)
  66. Structure and Stability of the Dimeric Triosephosphate Isomerase from the Thermophilic Archaeon Thermoplasma acidophilum. Park SH, Kim HS, Park MS, Moon S, Song MK, Park HS, Hahn H, Kim SJ, Bae E, Kim HJ, Han BW. PLoS One 10 e0145331 (2015)


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