메뉴 건너뛰기




Volumn 9, Issue 1, 2017, Pages 50-56

Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase

Author keywords

[No Author keywords available]

Indexed keywords

3-HYDROXYBUTANAL; ALDEHYDE; FRUCTOSE BISPHOSPHATE ALDOLASE;

EID: 85015318933     PISSN: 17554330     EISSN: 17554349     Source Type: Journal    
DOI: 10.1038/nchem.2596     Document Type: Article
Times cited : (237)

References (46)
  • 1
    • 0029444684 scopus 로고
    • Class i aldolases: Substrate specificity, mechanism, inhibitors and structural aspects
    • Gefflaut, T., Blonski, C., Perie, J. & Willson, M. Class I aldolases: substrate specificity, mechanism, inhibitors and structural aspects. Prog. Biophys. Mol. Biol. 63, 301-340 (1995).
    • (1995) Prog. Biophys. Mol. Biol. , vol.63 , pp. 301-340
    • Gefflaut, T.1    Blonski, C.2    Perie, J.3    Willson, M.4
  • 2
    • 34547178959 scopus 로고    scopus 로고
    • Recent advances in aldolasecatalyzed asymmetric synthesis
    • Dean, S. M., Greenberg, W. A. & Wong, C.-H. Recent advances in aldolasecatalyzed asymmetric synthesis. Adv. Synth. Catal. 349, 1308-1320 (2007).
    • (2007) Adv. Synth. Catal. , vol.349 , pp. 1308-1320
    • Dean, S.M.1    Greenberg, W.A.2    Wong, C.-H.3
  • 7
    • 18844456318 scopus 로고    scopus 로고
    • Development of small designer aldolase enzymes: Catalytic activity, folding, and substrate specificity
    • Tanaka, F., Fuller, R. & Barbas III, C. F. Development of small designer aldolase enzymes: catalytic activity, folding, and substrate specificity. Biochemistry 44, 7583-7592 (2005).
    • (2005) Biochemistry , vol.44 , pp. 7583-7592
    • Tanaka, F.1    Fuller, R.2    Barbas, C.F.3
  • 8
    • 0029590066 scopus 로고
    • Efficient aldolase catalytic antibodies that use the enamine mechanism of natural enzymes
    • Wagner, J., Lerner, R. A. & Barbas III, C. F. Efficient aldolase catalytic antibodies that use the enamine mechanism of natural enzymes. Science 270, 1797-1800 (1995).
    • (1995) Science , vol.270 , pp. 1797-1800
    • Wagner, J.1    Lerner, R.A.2    Barbas, C.F.3
  • 9
    • 0031457319 scopus 로고    scopus 로고
    • Immune versus natural selection: Antibody aldolases with enzymic rates but broader scope
    • Barbas III, C. F. et al. Immune versus natural selection: antibody aldolases with enzymic rates but broader scope. Science 278, 2085-2092 (1997).
    • (1997) Science , vol.278 , pp. 2085-2092
    • Barbas, C.F.1
  • 10
    • 40449116114 scopus 로고    scopus 로고
    • De novo computational design of retro-aldol enzymes
    • Jiang, L. et al. De novo computational design of retro-aldol enzymes. Science 319, 1387-1391 (2008).
    • (2008) Science , vol.319 , pp. 1387-1391
    • Jiang, L.1
  • 11
    • 84860115640 scopus 로고    scopus 로고
    • Robust design and optimization of retroaldol enzymes
    • Althoff, E. A. et al. Robust design and optimization of retroaldol enzymes. Protein Sci. 21, 717-726 (2012).
    • (2012) Protein Sci. , vol.21 , pp. 717-726
    • Althoff, E.A.1
  • 12
    • 84880920662 scopus 로고    scopus 로고
    • Evolution of a designed retro-aldolase leads to complete active site remodeling
    • Giger, L. et al. Evolution of a designed retro-aldolase leads to complete active site remodeling. Nat. Chem. Biol. 9, 494-498 (2013).
    • (2013) Nat. Chem. Biol. , vol.9 , pp. 494-498
    • Giger, L.1
  • 13
    • 84862212456 scopus 로고    scopus 로고
    • Droplet micro fluidics for high-throughput biological assays
    • Guo, M. T., Rotem, A., Heyman, J. A. & Weitz, D. A. Droplet microfluidics for high-throughput biological assays. Lab Chip 12, 2146-2155 (2012).
    • (2012) Lab Chip , vol.12 , pp. 2146-2155
    • Guo, M.T.1    Rotem, A.2    Heyman, J.A.3    Weitz, D.A.4
  • 14
    • 0031854986 scopus 로고    scopus 로고
    • Man-made cell-like compartments for molecular evolution
    • Tawfik, D. S. & Griffiths, A. D. Man-made cell-like compartments for molecular evolution. Nat. Biotechnol. 16, 652-656 (1998).
    • (1998) Nat. Biotechnol. , vol.16 , pp. 652-656
    • Tawfik, D.S.1    Griffiths, A.D.2
  • 15
    • 77749270677 scopus 로고    scopus 로고
    • Ultrahigh-throughput screening in drop-based microfluidics for directed evolution
    • Agresti, J. J. et al. Ultrahigh-throughput screening in drop-based microfluidics for directed evolution. Proc. Natl Acad. Sci. USA 107, 4004-4009 (2010).
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 4004-4009
    • Agresti, J.J.1
  • 16
    • 67649973848 scopus 로고    scopus 로고
    • Fluorescence-activated droplet sorting (FADS): Efficient microfluidic cell sorting based on enzymatic activity
    • Baret, J.-C. et al. Fluorescence-activated droplet sorting (FADS): efficient microfluidic cell sorting based on enzymatic activity. Lab Chip 9, 1850-1858 (2009).
    • (2009) Lab Chip , vol.9 , pp. 1850-1858
    • Baret, J.-C.1
  • 17
    • 84865492433 scopus 로고    scopus 로고
    • Picoliter cell lysate assays in microfluidic droplet compartments for directed enzyme evolution
    • Kintses, B. et al. Picoliter cell lysate assays in microfluidic droplet compartments for directed enzyme evolution. Chem. Biol. 19, 1001-1009 (2012).
    • (2012) Chem. Biol. , vol.19 , pp. 1001-1009
    • Kintses, B.1
  • 18
    • 65649102240 scopus 로고    scopus 로고
    • Reliable microfluidic on-chip incubation of droplets in delay-lines
    • Frenz, L., Blank, K., Brouzes, E. & Griffiths, A. D. Reliable microfluidic on-chip incubation of droplets in delay-lines. Lab Chip 9, 1344-1348 (2009).
    • (2009) Lab Chip , vol.9 , pp. 1344-1348
    • Frenz, L.1    Blank, K.2    Brouzes, E.3    Griffiths, A.D.4
  • 19
    • 84888034901 scopus 로고    scopus 로고
    • Precision is essential for efficient catalysis in an evolved Kemp eliminase
    • Blomberg, R. et al. Precision is essential for efficient catalysis in an evolved Kemp eliminase. Nature 503, 418-421 (2013).
    • (2013) Nature , vol.503 , pp. 418-421
    • Blomberg, R.1
  • 20
    • 0017058392 scopus 로고
    • Evolution of enzyme function and the development of catalytic efficiency
    • Albery, W. J. & Knowles, J. R. Evolution of enzyme function and the development of catalytic efficiency. Biochemistry 15, 5631-5640 (1976).
    • (1976) Biochemistry , vol.15 , pp. 5631-5640
    • Albery, W.J.1    Knowles, J.R.2
  • 21
    • 0037032455 scopus 로고    scopus 로고
    • Structural and functional analysis of aldolase B mutants related to hereditary fructose intolerance
    • Esposito, G. et al. Structural and functional analysis of aldolase B mutants related to hereditary fructose intolerance. FEBS Lett. 531, 152-156 (2002).
    • (2002) FEBS Lett. , vol.531 , pp. 152-156
    • Esposito, G.1
  • 22
    • 0035850820 scopus 로고    scopus 로고
    • Observation of covalent intermediates in an enzyme mechanism at atomic resolution
    • Heine, A. et al. Observation of covalent intermediates in an enzyme mechanism at atomic resolution. Science 294, 369-374 (2001).
    • (2001) Science , vol.294 , pp. 369-374
    • Heine, A.1
  • 23
    • 0034740575 scopus 로고    scopus 로고
    • Divergent evolution of (βα)8-barrel enzymes
    • Henn-Sax, M., Hocker, B., Wilmanns, M. & Sterner, R. Divergent evolution of (βα)8-barrel enzymes. Biol. Chem. 382, 1315-1320 (2001).
    • (2001) Biol. Chem. , vol.382 , pp. 1315-1320
    • Henn-Sax, M.1    Hocker, B.2    Wilmanns, M.3    Sterner, R.4
  • 24
    • 0036384350 scopus 로고    scopus 로고
    • One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures and functions
    • Nagano, N., Orengo, C. A. & Thornton, J. M. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J. Mol. Biol. 321, 741-765 (2002).
    • (2002) J. Mol. Biol. , vol.321 , pp. 741-765
    • Nagano, N.1    Orengo, C.A.2    Thornton, J.M.3
  • 25
    • 33947519204 scopus 로고    scopus 로고
    • Characterization, kinetics, and crystal structures of fructose-1,6-bisphosphate aldolase from the human parasite, Giardia lamblia
    • Galkin, A. et al. Characterization, kinetics, and crystal structures of fructose-1,6-bisphosphate aldolase from the human parasite, Giardia lamblia. J. Biol. Chem. 282, 4859-4867 (2007).
    • (2007) J. Biol. Chem. , vol.282 , pp. 4859-4867
    • Galkin, A.1
  • 26
    • 15544366696 scopus 로고    scopus 로고
    • Mechanism of the Schiff base forming fructose-1,6-bisphosphate aldolase: Structural analysis of reaction intermediates
    • Lorentzen, E., Siebers, B., Hensel, R. & Pohl, E. Mechanism of the Schiff base forming fructose-1,6-bisphosphate aldolase: structural analysis of reaction intermediates. Biochemistry 44, 4222-4229 (2005).
    • (2005) Biochemistry , vol.44 , pp. 4222-4229
    • Lorentzen, E.1    Siebers, B.2    Hensel, R.3    Pohl, E.4
  • 27
    • 77950437360 scopus 로고    scopus 로고
    • Origins of catalysis by computationally designed retroaldolase enzymes
    • Lassila, J. K., Baker, D. & Herschlag, D. Origins of catalysis by computationally designed retroaldolase enzymes. Proc. Natl Acad. Sci. USA 107, 4937-4942 (2010).
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 4937-4942
    • Lassila, J.K.1    Baker, D.2    Herschlag, D.3
  • 28
    • 84870921311 scopus 로고    scopus 로고
    • The use of enzymes in organic synthesis and the life sciences: Perspectives from the Swiss Industrial Biocatalysis Consortium (SIBC)
    • Meyer, H.-P. et al. The use of enzymes in organic synthesis and the life sciences: perspectives from the Swiss Industrial Biocatalysis Consortium (SIBC). Catal. Sci. Technol. 3, 29-40 (2013).
    • (2013) Catal. Sci. Technol. , vol.3 , pp. 29-40
    • Meyer, H.-P.1
  • 29
    • 84899486781 scopus 로고    scopus 로고
    • Design of activated serine-containing catalytic triads with atomic-level accuracy
    • Rajagopalan, S. et al. Design of activated serine-containing catalytic triads with atomic-level accuracy. Nat. Chem. Biol. 10, 386-391 (2014).
    • (2014) Nat. Chem. Biol. , vol.10 , pp. 386-391
    • Rajagopalan, S.1
  • 30
    • 84960296241 scopus 로고    scopus 로고
    • Mechanisms of protein evolution and their application to protein engineering
    • Glasner, M. E., Gerlt, J. A. & Babbitt, P. C. Mechanisms of protein evolution and their application to protein engineering. Adv. Enzymol. Areas Mol. Biol. 75, 193-239 (2007).
    • (2007) Adv. Enzymol. Areas Mol. Biol. , vol.75 , pp. 193-239
    • Glasner, M.E.1    Gerlt, J.A.2    Babbitt, P.C.3
  • 31
    • 84929497651 scopus 로고    scopus 로고
    • A promiscuous de novo retro-aldolase catalyzes asymmetric Michael additions via Schiff base intermediates
    • Garrabou, X., Beck, T. & Hilvert, D. A promiscuous de novo retro-aldolase catalyzes asymmetric Michael additions via Schiff base intermediates. Angew. Chem. Int. Ed. 54, 5609-5612 (2015).
    • (2015) Angew. Chem. Int. Ed. , vol.54 , pp. 5609-5612
    • Garrabou, X.1    Beck, T.2    Hilvert, D.3
  • 32
    • 84974589189 scopus 로고    scopus 로고
    • Fast Knoevenagel condensations catalyzed by an artificial Schiff-base-forming enzyme
    • Garrabou, X., Wicky, B. I. M. & Hilvert, D. Fast Knoevenagel condensations catalyzed by an artificial Schiff-base-forming enzyme. J. Am. Chem. Soc. 138, 6972-6974 (2016).
    • (2016) J. Am. Chem. Soc. , vol.138 , pp. 6972-6974
    • Garrabou, X.1    Wicky, B.I.M.2    Hilvert, D.3
  • 33
    • 84878935468 scopus 로고    scopus 로고
    • Design of protein catalysts
    • Hilvert, D. Design of protein catalysts. Annu. Rev. Biochem. 82, 447-470 (2013).
    • (2013) Annu. Rev. Biochem. , vol.82 , pp. 447-470
    • Hilvert, D.1
  • 34
    • 0035903602 scopus 로고    scopus 로고
    • Investigating and engineering enzymes by genetic selection
    • Taylor, S. V., Kast, P. & Hilvert, D. Investigating and engineering enzymes by genetic selection. Angew. Chem. Int. Ed. 40, 3310-3335 (2001).
    • (2001) Angew. Chem. Int. Ed. , vol.40 , pp. 3310-3335
    • Taylor, S.V.1    Kast, P.2    Hilvert, D.3
  • 35
    • 73149119826 scopus 로고    scopus 로고
    • Ultrahigh-throughput FACS-based screening for directed enzyme evolution
    • Yang, G. & Withers, S. G. Ultrahigh-throughput FACS-based screening for directed enzyme evolution. ChemBioChem 10, 2704-2715 (2009).
    • (2009) ChemBioChem , vol.10 , pp. 2704-2715
    • Yang, G.1    Withers, S.G.2
  • 36
    • 84900653348 scopus 로고    scopus 로고
    • One in a million: Flow cytometric sorting of single cell-lysate assays in monodisperse picolitre double emulsion droplets for directed evolution
    • Zinchenko, A. et al. One in a million: flow cytometric sorting of single cell-lysate assays in monodisperse picolitre double emulsion droplets for directed evolution. Anal. Chem. 86, 2526-2533 (2014).
    • (2014) Anal. Chem. , vol.86 , pp. 2526-2533
    • Zinchenko, A.1
  • 37
    • 84955206087 scopus 로고    scopus 로고
    • High-throughput analysis and protein engineering using microcapillary arrays
    • Chen, B. et al. High-throughput analysis and protein engineering using microcapillary arrays. Nat. Chem. Biol. 12, 76-81 (2016).
    • (2016) Nat. Chem. Biol. , vol.12 , pp. 76-81
    • Chen, B.1
  • 38
    • 2542563521 scopus 로고    scopus 로고
    • Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: Library construction methods for directed evolution
    • Neylon, C. Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution. Nucleic Acids Res. 32, 1448-1459 (2004).
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1448-1459
    • Neylon, C.1
  • 39
    • 0024556150 scopus 로고
    • Engineering hybrid genes without the use of restriction enzymes: Gene splicing by overlap extension
    • Horton, R. M., Hunt, H. D., Ho, S. N., Pullen, J. K. & Pease, L. R. Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene 77, 61-68 (1989).
    • (1989) Gene , vol.77 , pp. 61-68
    • Horton, R.M.1    Hunt, H.D.2    Ho, S.N.3    Pullen, J.K.4    Pease, L.R.5
  • 40
    • 34248632787 scopus 로고    scopus 로고
    • In vitro sexual evolution through the PCR-based staggered extension process (StEP)
    • Zhao, H. & Zha, W. In vitro sexual evolution through the PCR-based staggered extension process (StEP). Nat. Protocols 1, 1865-1871 (2006).
    • (2006) Nat. Protocols , vol.1 , pp. 1865-1871
    • Zhao, H.1    Zha, W.2
  • 41
    • 0028050350 scopus 로고
    • Rapid evolution of a protein in vitro by DNA shuffling
    • Stemmer, W. P. C. Rapid evolution of a protein in vitro by DNA shuffling. Nature 370, 389-391 (1994).
    • (1994) Nature , vol.370 , pp. 389-391
    • Stemmer, W.P.C.1
  • 42
    • 34447508216 scopus 로고    scopus 로고
    • Phaser crystallographic software
    • McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674 (2007).
    • (2007) J. Appl. Crystallogr. , vol.40 , pp. 658-674
    • McCoy, A.J.1
  • 43
    • 79953763877 scopus 로고    scopus 로고
    • REFMAC5 for the refinement of macromolecular crystal structures
    • Murshudov, G. N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D 67, 355-367 (2011).
    • (2011) Acta Crystallogr. D , vol.67 , pp. 355-367
    • Murshudov, G.N.1
  • 44
    • 37549039510 scopus 로고    scopus 로고
    • A short history of SHELX
    • Sheldrick, G.M. A short history of SHELX. Acta Crystallogr. A 64, 112-122 (2008).
    • (2008) Acta Crystallogr. A , vol.64 , pp. 112-122
    • Sheldrick, G.M.1
  • 45
    • 13244281317 scopus 로고    scopus 로고
    • COOT model-building tools for molecular graphics
    • Emsley, P. & Cowtan, K. COOT: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126-2132 (2004).
    • (2004) Acta Crystallogr. D , vol.60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 46
    • 7544226311 scopus 로고    scopus 로고
    • PRODRG: A tool for high-throughput crystallography of protein-ligand complexes
    • Schuttelkopf, A.W. & van Aalten, D. M. F. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D 60, 1355-1363 (2004).
    • (2004) Acta Crystallogr. D , vol.60 , pp. 1355-1363
    • Schuttelkopf, A.W.1    Van Aalten, D.M.F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.