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Structural determinants increasing flexibility confer cold adaptation in psychrophilic phosphoglycerate kinase

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Abstract

Crystal structures of phosphoglycerate kinase (PGK) from the psychrophile Pseudomonas sp. TACII 18 have been determined at high resolution by X-ray crystallography methods and compared with mesophilic, thermophilic and hyperthermophilic counterparts. PGK is a two-domain enzyme undergoing large domain movements to catalyze the production of ATP from 1,3-biphosphoglycerate and ADP. Whereas the conformational dynamics sustaining the catalytic mechanism of this hinge-bending enzyme now seems rather clear, the determinants which underlie high catalytic efficiency at low temperatures of this psychrophilic PGK were unknown. The comparison of the three-dimensional structures shows that multiple (global and local) specific adaptations have been brought about by this enzyme. Together, these reside in an overall increased flexibility of the cold-adapted PGK thereby allowing a better accessibility to the active site, but also a potentially more disordered transition state of the psychrophilic enzyme, due to the destabilization of some catalytic residues.

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Abbreviations

PGK:

Phosphoglycerate kinase

3-PG:

3-phosphoglycerate

1,3-PG:

1,3-bisphosphoglycerate

AMP-PNP:

Adenylyl imidophosphate

References

  • Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD (2012) Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr 68:352–367

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aghajari N, Feller G, Gerday C, Haser R (1998) Structures of the psychrophilic Alteromonas haloplanctis α-amylase give insights into cold adaptation at a molecular level. Structure 6:1503–1516

    Article  CAS  PubMed  Google Scholar 

  • Aghajari N, Van Petegem F, Villeret V, Chessa JP, Gerday C, Haser R, Van Beeumen J (2003) Crystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases. Proteins 50:636–647

    Article  CAS  PubMed  Google Scholar 

  • Auerbach G, Huber R, Grattinger M, Zaiss K, Schurig H, Jaenicke R, Jacob U (1997) Closed structure of phosphoglycerate kinase from Thermotoga maritima reveals the catalytic mechanism and determinants of thermal stability. Structure 5:1475–1483

    Article  CAS  PubMed  Google Scholar 

  • Baldwin E, Xu J, Hajiseyedjavadi O, Baase WA, Matthews BW (1996) Thermodynamic and structural compensation in “size-switch” core repacking variants of bacteriophage T4 lysozyme. J Mol Biol 259:542–559

    Article  CAS  PubMed  Google Scholar 

  • Banks RD, Blake CCF, Evans PR, Haser R, Rice DW, Hardy GW, Merrett M, Phillips AW (1979) Sequence, structure and activity of phosphoglycerate kinase: a possible hinge-bending enzyme. Nature 279:773–777

    Article  CAS  PubMed  Google Scholar 

  • Bentahir M, Feller G, Aittaleb M, Lamotte-Brasseur J, Himri T, Chessa JP, Gerday C (2000) Structural, kinetic, and calorimetric characterization of the cold-active phosphoglycerate kinase from the antarctic Pseudomonas sp. TACII18. J Biol Chem 275:11147–11153

    Article  CAS  PubMed  Google Scholar 

  • Bernstein BE, Hol WGJ (1997) Crystal structures of substrates and products bound to the phosphoglycerate kinase active site reveal the catalytic mechanism. Biochemistry 37:4429–4436

    Article  Google Scholar 

  • Bernstein BE, Williams DM, Bressi JC, Kuhn P, Gelb MH, Blackburn GM, Hol WGJ (1998) A bisubstrate analog induces unexpected conformational changes in phosphoglycerate kinase from Trypanosoma brucei. J Mol Biol 279:1137–1148

    Article  CAS  PubMed  Google Scholar 

  • Brünger AT (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355:472–475

    Article  PubMed  Google Scholar 

  • Burley SK, Petsko GA (1985) Aromatic-aromatic interaction: a mechanism of protein structure stabilization. Science 229:23–28

    Article  CAS  PubMed  Google Scholar 

  • Cliff MJ, Bowler MW, Varga A, Marston JP, Szabo J, Hounslow AM, Baxter NJ, Blackburn GM, Vas M, Waltho JP (2010) Transition state analogue structures of human phosphoglycerate kinase establish the importance of charge balance in catalysis. J Am Chem Soc 132:6507–6516

    Article  CAS  PubMed  Google Scholar 

  • Combet C, Blanchet C, Geourjon C, Deleage G (2000) NPS@: network protein sequence analysis. Trends Biochem Sci 25:147–150

    Article  CAS  PubMed  Google Scholar 

  • Creighton TE (1991) Stability of folded conformations. Curr Opin Struct Biol 1:5–16

    Article  CAS  Google Scholar 

  • Davies GJ, Gamblin SJ, Littlechild JA, Watson HC (1993) The structure of a thermally stable 3-phosphoglycerate kinase and a comparison with its mesophilic equivalent. Proteins 15:283–289

    Article  CAS  PubMed  Google Scholar 

  • DeLano WL (2002) PyMOL. DeLano scientific, San Carlos, p 700

    Google Scholar 

  • Dill KA (1990) The meaning of hydrophobicity. Science 250:297–298

    Article  CAS  PubMed  Google Scholar 

  • Emsley P, Lohkamp B, Scott WG, Cowtan G (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66:486–501

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Feller G (2013) Psychrophilic enzymes: from folding to function and biotechnology. Scientifica (Cairo), 512840

  • Feller G, Gerday C (2003) Psychrophilic enzymes: hot topics in cold adaptation. Nat Rev Microbiol 1:200–208

    Article  CAS  PubMed  Google Scholar 

  • 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 (2000) Cold-adapted enzymes: from fundamentals to biotechnology. Trends Biotechnol 18:103–107

    Article  CAS  PubMed  Google Scholar 

  • Harlos K, Vas M, Blake CFF (1992) Crystal structure of the binary complex of pig muscle phosphoglycerate kinase and its substrate 3-phospho-D-glycerate. Proteins 12:133–144

    Article  CAS  PubMed  Google Scholar 

  • Hess D, Kruger K, Knappik A, Palm P, Hensel R (1995) Dimeric 3-phosphoglycerate kinases from hyperthermophilic Archaea. Cloning, sequencing and expression of the 3-phosphoglycerate kinase gene of Pyrococcus woesei in Escherichia coli and characterization of the protein. Structural and functional comparison with the 3-phosphoglycerate kinase of Methanothermus fervidus. Eur J Biochem 233:227–237

    Article  CAS  PubMed  Google Scholar 

  • Inoue R, Biehl R, Rosenkranz T, Fitter J, Monkenbush M, Radulescu A, Farago B, Richter D (2010) Large domain fluctuations on 50-ns timescale enable catalytic activity in phosphoglycerate kinase. Biophys J 99:2309–2317

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jaenicke R (1990) Protein structure and function at low temperatures. Philos Trans R Soc Lond B Biol Sci 326:535–551

    Article  CAS  PubMed  Google Scholar 

  • Jaenicke R, Bohm G (1998) The stability of proteins in extreme environments. Curr Opin Struct Biol 8:738–748

    Article  CAS  PubMed  Google Scholar 

  • Jones CE, Fleming TM, Cowan DA, Littlechild JA, Piper PW (1995) The phosphoglycerate kinase and glyceraldehyde-3-phosphate dehydrogenase genes from the thermophilic archaeon Sulfolobus solfataricus overlap by 8-bp. Isolation, sequencing of the genes and expression in Escherichia coli. Eur J Biochem 233:800–808

    Article  CAS  PubMed  Google Scholar 

  • Kabsch W, Sander C (1983) Biopolymers 22:2577–2637

    Article  CAS  PubMed  Google Scholar 

  • Krissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60:2256–2268

    Article  CAS  PubMed  Google Scholar 

  • Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26:283–291

    Article  CAS  Google Scholar 

  • Low PS, Bada JL, Somero GN (1973) Temperature adaptation of enzymes: roles of the free energy, the enthalpy, and the entropy of activation. Proc Natl Acad Sci U S A 70:430–432

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mandelman D, Bentahir M, Feller G, Gerday C, Haser R (2001) Crystallization and preliminary X-ray analysis of a bacterial psychrophilic enzyme, phosphoglycerate kinase. Acta Crystallogr D Biol Crystallogr 257:1666–1668

    Article  Google Scholar 

  • Marston JP, Cliff MJ, Reed MAC, Blackburn GM, Hounslow AM, Craven CJ, Waltho JP (2010) Structural tightening and interdomain communication in the catalytic cycle of phosphoglycerate kinase. J Mol Biol 396:345–360

    Article  CAS  PubMed  Google Scholar 

  • Matthews BW (1968) Solvent content of protein crystals. J Mol Biol 33:491–497

    Article  CAS  PubMed  Google Scholar 

  • McDonald IK, Thornton JM (1994) Satisfying hydrogen bonding potential in proteins. J Mol Biol 238:777–793

    Article  CAS  PubMed  Google Scholar 

  • Mykytczuk NC, Foote SJ, Omelon CR, Southam G, Greer CW, Whyte LG (2013) Bacterial growth at −15 degrees C; molecular insights from the permafrost bacterium Planococcus halocryophilus Or1. ISME J 7:1211–1226

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Navaza J (2001) Implementation of molecular replacement in AMoRe. Acta Crystallogr D Biol Crystallogr 57:1367–1372

    Article  CAS  PubMed  Google Scholar 

  • Nicholls AJ (1993) GRASP: graphical representation and analysis of surface properties. Biophys J 64:A116

    Google Scholar 

  • Otwinoswki Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307–326

    Article  Google Scholar 

  • Parker MJ, Spencer J, Jackson GS, Burston SG, Hosszu LLP, Craven CJ, Waltho JP, Clarke AR (1996) Domain behaviour during the folding of a thermostable phosphoglycerate kinase. Biochemistry 35:15740–15752

    Article  CAS  PubMed  Google Scholar 

  • Privalov L, Gill SJ (1988) Stability of protein structure and hydrophobic interaction. Adv Protein Chem 39:191–234

    Article  CAS  PubMed  Google Scholar 

  • Ramakrishnan C, Ramachandran GN (1965) Stereochemical criteria for polypeptide and protein chain conformations. Biophys J 5:909–933

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Robert X, Gouet P (2014) Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res 42:W320–W324

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Russell RJ, Gerike U, Danson MJ, Hough DW, Taylor GL (1998) Structural adaptations of the cold-active citrate synthase from an Antarctic bacterium. Structure 6:351–361

    Article  CAS  PubMed  Google Scholar 

  • Siddiqui KS, Cavicchioli R (2006) Cold-adapted enzymes. Annu Rev Biochem 75:403–433

    Article  CAS  PubMed  Google Scholar 

  • Smalås AO, Leiros HK, Os V, Willassen NP (2000) Cold adapted enzymes. Biotechnol Annu Rev 6:1–57

    Article  PubMed  Google Scholar 

  • Srere PA (1987) Complexes of sequential metabolic enzymes. Annu Rev Biochem 56:89–124

    Article  CAS  PubMed  Google Scholar 

  • Srivastava DK, Bernhard SA (1986) Metabolite transfer via enzyme–enzyme complexes. Science 234:1081–1086

    Article  CAS  PubMed  Google Scholar 

  • Struvay C, Feller G (2012) Optimization to low temperature activity in psychrophilic enzymes. Int J Mol Sci 13:11643–11665

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sukenik S, Ren P, Gruebele M (2017) Weak protein-protein interactions in live cells are quantified by cell-volume modulation. PNAS 114:6776–6781

    CAS  PubMed  PubMed Central  Google Scholar 

  • Takai K, Nakamura K, Toki T, Tsunogai U, Miyazaki M, Miyazaki J, Hirayama H, Nakagawa S, Nunoura T, Horikoshi K (2008) Cell proliferation at 122 C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation. Proc Natl Acad Sci U S A 105:10949–10954

    Article  PubMed  PubMed Central  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tina KG, Bhadra R, Srinivasan N (2007) PIC: protein Interactions Calculator. Nucleic Acid Res 35:W473–W476

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tomokuni Y, Goryo K, Katsura A, Torii S, Yasumoto K, Kemnitz K, Takada M, Fukumura H, Sogawa K (2010) Loose interaction between glyceraldehyde-3-phosphate dehydrogenase and phosphoglycerate kinase revealed by fluorescence resonance energy transfer-fluorescence lifetime imaging microscopy in living cells. FEBS J 277:1310–1318

    Article  CAS  PubMed  Google Scholar 

  • Van Dijk E, Varilly P, Knowles TPJ, Frenkel D, Abeln S (2016) Consistent treatment of hydrophobicity in protein lattice models accounts for cold denaturation. Phys Rev Lett 116:078101

    Article  CAS  PubMed  Google Scholar 

  • Watanabe K, Hata Y, Kizaki H, Katsube Y, Suzuki Y (1997) The refined crystal structure of Bacillus cereus oligo-1,6-glucosidase at 2.0 Å resolution: structural characterization of proline substitution sites for protein stabilization. J Mol Biol 269:142–153

    Article  CAS  PubMed  Google Scholar 

  • Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AGW, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67:235–242

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yip KSP, Stillman TJ, Britton KL, Artymiuk PJ, Baker PJ, Sedelnikova SE, Engel PC, Pasquo A, Chiaraluce R, Consalvi V, Scandurra R, Rice DW (1995) The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures. Structure 3:1147–1158

    Article  CAS  PubMed  Google Scholar 

  • Zecchinon L, Oriol A, Netzel U, Svennberg J, Gerardin-Otthiers N, Feller G (2005) Stability domains, substrate-induced conformational changes, and hinge-bending motions in a psychrophilic phosphoglycerate kinase. A microcalorimetric study. J Biol Chem 280:41307–41314

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This work was supported by the Centre National de la Recherche Scientifique, by the European Union under the form of a TMR contract CT970131 (ColdNet), and by the Fonds National de la Recherche Scientifique, Belgium (Grants to GF and CG).

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Author notes

  1. David Mandelman, Lionel Ballut, and David A. Wolff contributed equally to this work.

Authors and Affiliations

  1. Biocrystallography and Structural Biology of Therapeutic Targets, Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS, University of Lyon 1, 7 passage du Vercors, 69367, Lyon Cedex 07, France

    David Mandelman, Lionel Ballut, David A. Wolff, Richard Haser & Nushin Aghajari

  2. Laboratory of Biochemistry, Center for Protein Engineering - InBioS, Institute of Chemistry B6a, University of Liège, Sart-Tilman, 4000, Liège, Belgium

    Georges Feller & Charles Gerday

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  1. David Mandelman
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  2. Lionel Ballut
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Correspondence to Nushin Aghajari.

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Mandelman, D., Ballut, L., Wolff, D.A. et al. Structural determinants increasing flexibility confer cold adaptation in psychrophilic phosphoglycerate kinase. Extremophiles 23, 495–506 (2019). https://doi.org/10.1007/s00792-019-01102-x

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