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Volumn 378, Issue 3, 2008, Pages 666-672

Engineering Protein Allostery: 1.05 Å Resolution Structure and Enzymatic Properties of a Na+-activated Trypsin

Author keywords

allostery; crystal structure; monovalent cation activation; sodium; trypsin

Indexed keywords

BLOOD CLOTTING FACTOR 10A; SODIUM ION; TRYPSIN;

EID: 42249106210     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.03.003     Document Type: Article
Times cited : (15)

References (48)
  • 1
    • 0036882394 scopus 로고    scopus 로고
    • Serine protease mechanism and specificity
    • Hedstrom L. Serine protease mechanism and specificity. Chem. Rev. 102 (2002) 4501-4524
    • (2002) Chem. Rev. , vol.102 , pp. 4501-4524
    • Hedstrom, L.1
  • 2
    • 42249109450 scopus 로고    scopus 로고
    • Serine peptidases: classification, structure and function
    • Page M.J., and Di Cera E. Serine peptidases: classification, structure and function. Cell Mol. Life Sci. 65 (2008) 1220-1236
    • (2008) Cell Mol. Life Sci. , vol.65 , pp. 1220-1236
    • Page, M.J.1    Di Cera, E.2
  • 3
    • 33644686444 scopus 로고    scopus 로고
    • A structural perspective on enzymes activated by monovalent cations
    • Di Cera E. A structural perspective on enzymes activated by monovalent cations. J. Biol. Chem. 281 (2006) 1305-1308
    • (2006) J. Biol. Chem. , vol.281 , pp. 1305-1308
    • Di Cera, E.1
  • 4
    • 33745299907 scopus 로고    scopus 로고
    • Role of Na+ and K+ in enzyme function
    • Page M.J., and Di Cera E. Role of Na+ and K+ in enzyme function. Physiol. Rev. 86 (2006) 1049-1092
    • (2006) Physiol. Rev. , vol.86 , pp. 1049-1092
    • Page, M.J.1    Di Cera, E.2
  • 5
    • 0029785840 scopus 로고    scopus 로고
    • Residue 225 determines the Na(+)-induced allosteric regulation of catalytic activity in serine proteases
    • Dang Q.D., and Di Cera E. Residue 225 determines the Na(+)-induced allosteric regulation of catalytic activity in serine proteases. Proc. Natl Acad. Sci. USA 93 (1996) 10653-10656
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 10653-10656
    • Dang, Q.D.1    Di Cera, E.2
  • 6
    • 0035876166 scopus 로고    scopus 로고
    • Molecular markers of serine protease evolution
    • Krem M.M., and Di Cera E. Molecular markers of serine protease evolution. EMBO J. 20 (2001) 3036-3045
    • (2001) EMBO J. , vol.20 , pp. 3036-3045
    • Krem, M.M.1    Di Cera, E.2
  • 7
    • 0033214037 scopus 로고    scopus 로고
    • The C-terminal sequence encodes function in serine proteases
    • Krem M.M., Rose T., and Di Cera E. The C-terminal sequence encodes function in serine proteases. J. Biol. Chem. 274 (1999) 28063-28066
    • (1999) J. Biol. Chem. , vol.274 , pp. 28063-28066
    • Krem, M.M.1    Rose, T.2    Di Cera, E.3
  • 12
    • 1642269650 scopus 로고    scopus 로고
    • Residue Asp-189 controls both substrate binding and the monovalent cation specificity of thrombin
    • Prasad S., Cantwell A.M., Bush L.A., Shih P., Xu H., and Di Cera E. Residue Asp-189 controls both substrate binding and the monovalent cation specificity of thrombin. J. Biol. Chem. 279 (2004) 10103-10108
    • (2004) J. Biol. Chem. , vol.279 , pp. 10103-10108
    • Prasad, S.1    Cantwell, A.M.2    Bush, L.A.3    Shih, P.4    Xu, H.5    Di Cera, E.6
  • 13
    • 0033582504 scopus 로고    scopus 로고
    • Identification and characterization of the sodium-binding site of activated protein C
    • He X., and Rezaie A.R. Identification and characterization of the sodium-binding site of activated protein C. J. Biol. Chem. 274 (1999) 4970-4976
    • (1999) J. Biol. Chem. , vol.274 , pp. 4970-4976
    • He, X.1    Rezaie, A.R.2
  • 14
    • 0034727531 scopus 로고    scopus 로고
    • Role of residue Phe225 in the cofactor-mediated, allosteric regulation of the serine protease coagulation factor VIIa
    • Petrovan R.J., and Ruf W. Role of residue Phe225 in the cofactor-mediated, allosteric regulation of the serine protease coagulation factor VIIa. Biochemistry 39 (2000) 14457-14463
    • (2000) Biochemistry , vol.39 , pp. 14457-14463
    • Petrovan, R.J.1    Ruf, W.2
  • 15
    • 0034701009 scopus 로고    scopus 로고
    • Sodium binding site of factor Xa: role of sodium in the prothrombinase complex
    • Rezaie A.R., and He X. Sodium binding site of factor Xa: role of sodium in the prothrombinase complex. Biochemistry 39 (2000) 1817-1825
    • (2000) Biochemistry , vol.39 , pp. 1817-1825
    • Rezaie, A.R.1    He, X.2
  • 16
    • 0032461837 scopus 로고    scopus 로고
    • Role of P225 and the C136-C201 disulfide bond in tissue plasminogen activator
    • Vindigni A., and Di Cera E. Role of P225 and the C136-C201 disulfide bond in tissue plasminogen activator. Protein Sci. 7 (1998) 1728-1737
    • (1998) Protein Sci. , vol.7 , pp. 1728-1737
    • Vindigni, A.1    Di Cera, E.2
  • 18
    • 9944263528 scopus 로고    scopus 로고
    • Searching for new allosteric sites in enzymes
    • Hardy J.A., and Wells J.A. Searching for new allosteric sites in enzymes. Curr. Opin. Struct. Biol. 14 (2004) 706-715
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 706-715
    • Hardy, J.A.1    Wells, J.A.2
  • 19
    • 32344434479 scopus 로고    scopus 로고
    • The changing landscape of protein allostery
    • Swain J.F., and Gierasch L.M. The changing landscape of protein allostery. Curr. Opin. Struct. Biol. 16 (2006) 102-108
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 102-108
    • Swain, J.F.1    Gierasch, L.M.2
  • 21
    • 33751539464 scopus 로고    scopus 로고
    • Protein-protein interactions in the allosteric regulation of protein kinases
    • Pellicena P., and Kuriyan J. Protein-protein interactions in the allosteric regulation of protein kinases. Curr. Opin. Struct. Biol. 16 (2006) 702-709
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 702-709
    • Pellicena, P.1    Kuriyan, J.2
  • 22
    • 41149167073 scopus 로고    scopus 로고
    • Structural identification of the pathway of long-range communication in an allosteric enzyme
    • Gandhi P.S., Chen Z., Mathews F.S., and Di Cera E. Structural identification of the pathway of long-range communication in an allosteric enzyme. Proc. Natl Acad. Sci. USA 105 (2008) 1832-1837
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 1832-1837
    • Gandhi, P.S.1    Chen, Z.2    Mathews, F.S.3    Di Cera, E.4
  • 23
    • 0034711284 scopus 로고    scopus 로고
    • Thermodynamic linkage between the S1 site, the Na+ site, and the Ca2+ site in the protease domain of human coagulation factor xa. Studies on catalytic efficiency and inhibitor binding
    • Underwood M.C., Zhong D., Mathur A., Heyduk T., and Bajaj S.P. Thermodynamic linkage between the S1 site, the Na+ site, and the Ca2+ site in the protease domain of human coagulation factor xa. Studies on catalytic efficiency and inhibitor binding. J. Biol. Chem. 275 (2000) 36876-36884
    • (2000) J. Biol. Chem. , vol.275 , pp. 36876-36884
    • Underwood, M.C.1    Zhong, D.2    Mathur, A.3    Heyduk, T.4    Bajaj, S.P.5
  • 24
    • 0030848495 scopus 로고    scopus 로고
    • Site-specific dissection of substrate recognition by thrombin
    • Vindigni A., Dang Q.D., and Di Cera E. Site-specific dissection of substrate recognition by thrombin. Nature Biotechnol. 15 (1997) 891-895
    • (1997) Nature Biotechnol. , vol.15 , pp. 891-895
    • Vindigni, A.1    Dang, Q.D.2    Di Cera, E.3
  • 25
    • 0041664882 scopus 로고    scopus 로고
    • Engineering the primary substrate specificity of Streptomyces griseus trypsin
    • Page M.J., Wong S.L., Hewitt J., Strynadka N.C., and MacGillivray R.T. Engineering the primary substrate specificity of Streptomyces griseus trypsin. Biochemistry 42 (2003) 9060-9066
    • (2003) Biochemistry , vol.42 , pp. 9060-9066
    • Page, M.J.1    Wong, S.L.2    Hewitt, J.3    Strynadka, N.C.4    MacGillivray, R.T.5
  • 26
    • 0023881841 scopus 로고
    • Refined crystal structure of Streptomyces griseus trypsin at 1.7 Å resolution
    • Read R.J., and James M.N. Refined crystal structure of Streptomyces griseus trypsin at 1.7 Å resolution. J. Mol. Biol. 200 (1988) 523-551
    • (1988) J. Mol. Biol. , vol.200 , pp. 523-551
    • Read, R.J.1    James, M.N.2
  • 28
    • 22744448212 scopus 로고    scopus 로고
    • Quantification of cation-pi interactions in protein-ligand complexes: crystal-structure analysis of Factor Xa bound to a quaternary ammonium ion ligand
    • Scharer K., Morgenthaler M., Paulini R., Obst-Sander U., Banner D.W., Schlatter D., et al. Quantification of cation-pi interactions in protein-ligand complexes: crystal-structure analysis of Factor Xa bound to a quaternary ammonium ion ligand. Angew Chem. Int. Ed. Engl. 44 (2005) 4400-4404
    • (2005) Angew Chem. Int. Ed. Engl. , vol.44 , pp. 4400-4404
    • Scharer, K.1    Morgenthaler, M.2    Paulini, R.3    Obst-Sander, U.4    Banner, D.W.5    Schlatter, D.6
  • 29
    • 0030935412 scopus 로고    scopus 로고
    • The molecular environment of the Na+ binding site of thrombin
    • Zhang E., and Tulinsky A. The molecular environment of the Na+ binding site of thrombin. Biophys. Chem. 63 (1997) 185-200
    • (1997) Biophys. Chem. , vol.63 , pp. 185-200
    • Zhang, E.1    Tulinsky, A.2
  • 30
    • 0036014793 scopus 로고    scopus 로고
    • Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium
    • Harding M.M. Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium. Acta Crystallogr. D 58 (2002) 872-874
    • (2002) Acta Crystallogr. D , vol.58 , pp. 872-874
    • Harding, M.M.1
  • 31
    • 0000020840 scopus 로고
    • Empirical parameters for calculating cation-oxygen bond valence
    • Brown I.D., and Wu K.K. Empirical parameters for calculating cation-oxygen bond valence. Acta Crystallogr. B 32 (1976) 1957-1959
    • (1976) Acta Crystallogr. B , vol.32 , pp. 1957-1959
    • Brown, I.D.1    Wu, K.K.2
  • 32
    • 0028179634 scopus 로고
    • Predicting Ca(2+)-binding sites in proteins
    • Nayal M., and Di Cera E. Predicting Ca(2+)-binding sites in proteins. Proc. Natl Acad. Sci. USA 91 (1994) 817-821
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 817-821
    • Nayal, M.1    Di Cera, E.2
  • 33
    • 0029926326 scopus 로고    scopus 로고
    • Valence screening of water in protein crystals reveals potential Na+ binding sites
    • Nayal M., and Di Cera E. Valence screening of water in protein crystals reveals potential Na+ binding sites. J. Mol. Biol. 256 (1996) 228-234
    • (1996) J. Mol. Biol. , vol.256 , pp. 228-234
    • Nayal, M.1    Di Cera, E.2
  • 34
    • 0028133496 scopus 로고
    • Converting trypsin to chymotrypsin: residue 172 is a substrate specificity determinant
    • Hedstrom L., Perona J.J., and Rutter W.J. Converting trypsin to chymotrypsin: residue 172 is a substrate specificity determinant. Biochemistry 33 (1994) 8757-8763
    • (1994) Biochemistry , vol.33 , pp. 8757-8763
    • Hedstrom, L.1    Perona, J.J.2    Rutter, W.J.3
  • 35
    • 0027965324 scopus 로고
    • Converting trypsin to chymotrypsin: ground-state binding does not determine substrate specificity
    • Hedstrom L., Farr-Jones S., Kettner C.A., and Rutter W.J. Converting trypsin to chymotrypsin: ground-state binding does not determine substrate specificity. Biochemistry 33 (1994) 8764-8769
    • (1994) Biochemistry , vol.33 , pp. 8764-8769
    • Hedstrom, L.1    Farr-Jones, S.2    Kettner, C.A.3    Rutter, W.J.4
  • 36
    • 0026520387 scopus 로고
    • Converting trypsin to chymotrypsin: the role of surface loops
    • Hedstrom L., Szilagyi L., and Rutter W.J. Converting trypsin to chymotrypsin: the role of surface loops. Science 255 (1992) 1249-1253
    • (1992) Science , vol.255 , pp. 1249-1253
    • Hedstrom, L.1    Szilagyi, L.2    Rutter, W.J.3
  • 37
    • 0346022974 scopus 로고    scopus 로고
    • Understanding protein-ligand interactions: the price of protein flexibility
    • Rauh D., Klebe G., and Stubbs M.T. Understanding protein-ligand interactions: the price of protein flexibility. J. Mol. Biol. 335 (2004) 1325-1341
    • (2004) J. Mol. Biol. , vol.335 , pp. 1325-1341
    • Rauh, D.1    Klebe, G.2    Stubbs, M.T.3
  • 38
    • 0041743079 scopus 로고    scopus 로고
    • ZZ made EZ: influence of inhibitor configuration on enzyme selectivity
    • Rauh D., Klebe G., Sturzebecher J., and Stubbs M.T. ZZ made EZ: influence of inhibitor configuration on enzyme selectivity. J. Mol. Biol. 330 (2003) 761-770
    • (2003) J. Mol. Biol. , vol.330 , pp. 761-770
    • Rauh, D.1    Klebe, G.2    Sturzebecher, J.3    Stubbs, M.T.4
  • 39
    • 0036661079 scopus 로고    scopus 로고
    • Trypsin mutants for structure-based drug design: expression, refolding and crystallisation
    • Rauh D., Reyda S., Klebe G., and Stubbs M.T. Trypsin mutants for structure-based drug design: expression, refolding and crystallisation. Biol. Chem. 383 (2002) 1309-1314
    • (2002) Biol. Chem. , vol.383 , pp. 1309-1314
    • Rauh, D.1    Reyda, S.2    Klebe, G.3    Stubbs, M.T.4
  • 40
    • 41849107110 scopus 로고    scopus 로고
    • Understanding binding selectivity toward trypsin and factor Xa: the role of aromatic interactions
    • Di Fenza A., Heine A., Koert U., and Klebe G. Understanding binding selectivity toward trypsin and factor Xa: the role of aromatic interactions. ChemMedChem 2 (2007) 297-308
    • (2007) ChemMedChem , vol.2 , pp. 297-308
    • Di Fenza, A.1    Heine, A.2    Koert, U.3    Klebe, G.4
  • 41
    • 0037474479 scopus 로고    scopus 로고
    • Reconstructing the binding site of factor Xa in trypsin reveals ligand-induced structural plasticity
    • Reyda S., Sohn C., Klebe G., Rall K., Ullmann D., Jakubke H.D., and Stubbs M.T. Reconstructing the binding site of factor Xa in trypsin reveals ligand-induced structural plasticity. J. Mol. Biol. 325 (2003) 963-977
    • (2003) J. Mol. Biol. , vol.325 , pp. 963-977
    • Reyda, S.1    Sohn, C.2    Klebe, G.3    Rall, K.4    Ullmann, D.5    Jakubke, H.D.6    Stubbs, M.T.7
  • 42
    • 33846031987 scopus 로고    scopus 로고
    • Rapid kinetics of Na+ binding to thrombin
    • Bah A., Garvey L.C., Ge J., and Di Cera E. Rapid kinetics of Na+ binding to thrombin. J. Biol. Chem. 281 (2006) 40049-40056
    • (2006) J. Biol. Chem. , vol.281 , pp. 40049-40056
    • Bah, A.1    Garvey, L.C.2    Ge, J.3    Di Cera, E.4
  • 43
    • 0031745764 scopus 로고    scopus 로고
    • Site-specific analysis of mutational effects in proteins
    • Di Cera E. Site-specific analysis of mutational effects in proteins. Adv. Protein Chem. 51 (1998) 59-119
    • (1998) Adv. Protein Chem. , vol.51 , pp. 59-119
    • Di Cera, E.1
  • 44
    • 0031059866 scopus 로고    scopus 로고
    • Processing of x-ray diffraction data collected by oscillation methods
    • Otwinowski Z., and Minor W. Processing of x-ray diffraction data collected by oscillation methods. Methods Enzymol. 276 (1997) 307-326
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 46
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53 (1997) 240-255
    • (1997) Acta Crystallogr. D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 47
    • 0030880598 scopus 로고    scopus 로고
    • SHELXL: high-resolution refinement
    • Sheldrick G., and Schneider T. SHELXL: high-resolution refinement. Methods Enzymol. 277 (1997) 319-343
    • (1997) Methods Enzymol. , vol.277 , pp. 319-343
    • Sheldrick, G.1    Schneider, T.2
  • 48
    • 13244281317 scopus 로고    scopus 로고
    • Coot: model-building tools for molecular graphics
    • Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60 (2004) 2126-2132
    • (2004) Acta Crystallogr. D , vol.60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2


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