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Korean Society for Biochemistry and Molecular Biology (생화학분자생물학회)
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Crystallographic snapshots of active site metal shift in E. coli fructose 1,6-bisphosphate aldolase

  • Tran, Huyen-Thi (Department of Biological Sciences, Konkuk University) ;
  • Lee, Seon-Hwa (Department of Bioscience and Biotechnology, Konkuk University) ;
  • Ho, Thien-Hoang (Department of Biological Sciences, Konkuk University) ;
  • Hong, Seung-Hye (Department of Bioscience and Biotechnology, Konkuk University) ;
  • Huynh, Kim-Hung (Department of Biological Sciences, Konkuk University) ;
  • Ahn, Yeh-Jin (Department of Life Science, Sangmyung University) ;
  • Oh, Deok-Kun (Department of Bioscience and Biotechnology, Konkuk University) ;
  • Kang, Lin-Woo (Department of Biological Sciences, Konkuk University)
  • Received : 2016.08.04
  • Accepted : 2016.10.10
  • Published : 2016.12.31
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Abstract

Fructose 1,6-bisphosphate aldolase (FBA) is important for both glycolysis and gluconeogenesis in life. Class II (zinc dependent) FBA is an attractive target for the development of antibiotics against protozoa, bacteria, and fungi, and is also widely used to produce various high-value stereoisomers in the chemical and pharmaceutical industry. In this study, the crystal structures of class II Escherichia coli FBA (EcFBA) were determined from four different crystals, with resolutions between $1.8{\AA}$ and $2.0{\AA}$. Native EcFBA structures showed two separate sites of Zn1 (interior position) and Zn2 (active site surface position) for $Zn^{2+}$ ion. Citrate and TRIS bound EcFBA structures showed $Zn^{2+}$ position exclusively at Zn2. Crystallographic snapshots of EcFBA structures with and without ligand binding proposed the rationale of metal shift at the active site, which might be a hidden mechanism to keep the trace metal cofactor $Zn^{2+}$ within EcFBA without losing it.

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References

  1. Lorentzen E, Siebers B, Hensel R and Pohl E (2005) Crystal structure of an archaeal class I aldolase and the evolution of (betaalpha)8 barrel proteins. Biochemistry 44, 4222-4229 https://doi.org/10.1021/bi048192o
  2. Hall DR, Leonard GA, Reed CD, Watt CI, Berry A and Hunter WN (1999) The crystal structure of Escherichia coli class II fructose-1, 6-bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity. J Mol Biol 287, 383-394 https://doi.org/10.1006/jmbi.1999.2609
  3. Marsh JJ and Lebherz HG (1992) Fructose-bisphosphate aldolases: an evolutionary history. Trends Biochem Sci 17, 110-113 https://doi.org/10.1016/0968-0004(92)90247-7
  4. Pegan SD, Rukseree K, Franzblau SG and Mesecar AD (2009) Structural basis for catalysis of a tetrameric class IIa fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis. J Mol Biol 386, 1038-1053 https://doi.org/10.1016/j.jmb.2009.01.003
  5. Gerdes SY, Scholle MD, Campbell JW et al (2003) Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol 185, 5673-5684 https://doi.org/10.1128/JB.185.19.5673-5684.2003
  6. Wehmeier UF (2001) Molecular cloning, nucleotide sequence and structural analysis of the Streptomyces galbus DSM40480 fda gene: the S. galbus fructose-1,6-bisphosphate aldolase is a member of the class II aldolases. FEMS Microbiol Lett 197, 53-58 https://doi.org/10.1111/j.1574-6968.2001.tb10582.x
  7. Wagner J, Lerner RA and Barbas CF (1995) Efficient aldolase catalytic antibodies that use the enamine mechanism of natural enzymes. Science 270, 1797-1800 https://doi.org/10.1126/science.270.5243.1797
  8. Von der Osten CH, Sinskey AJ, Barbas CF, Pederson RL, Wang YF and Wong CH (1989) Use of a recombinant bacterial fructose-1, 6-diphosphate aldolase in aldol reactions: preparative syntheses of 1-deoxynojirimycin, 1-deoxymannojirimycin, 1, 4-dideoxy-1, 4-imino-D-arabinitol, and fagomine. J Am Chem Soc 111, 3924-3927 https://doi.org/10.1021/ja00193a025
  9. Liu J, Hsu C-C and Wong C-H (2004) Sequential aldol condensation catalyzed by DERA mutant Ser238Asp and a formal total synthesis of atorvastatin. Tetrahedron Lett 45, 2439-2441 https://doi.org/10.1016/j.tetlet.2004.01.110
  10. Blom NS, Tetreault S, Coulombe R and Sygusch J (1996) Novel active site in Escherichia coli fructose 1,6-bisphosphate aldolase. Nat Struct Biol 3, 856-862 https://doi.org/10.1038/nsb1096-856
  11. Galkin A, Li Z, Li L et al (2009) Structural insights into the substrate binding and stereoselectivity of giardia fructose-1,6-bisphosphate aldolase Biochemistry 48, 3186-3196 https://doi.org/10.1021/bi9001166
  12. Daher R, Coincon M, Fonvielle M et al (2010) Rational design, synthesis, and evaluation of new selective inhibitors of microbial class II (zinc dependent) fructose bis-phosphate aldolases. J Med Chem 53, 7836-7842 https://doi.org/10.1021/jm1009814
  13. Capodagli GC, Sedhom WG, Jackson M, Ahrendt KA and Pegan SD (2014) A noncompetitive inhibitor for Mycobacterium tuberculosis's class IIa fructose 1,6-bisphosphate aldolase. Biochemistry 53, 202-213 https://doi.org/10.1021/bi401022b
  14. Capodagli GC, Lee SA, Boehm KJ, Brady KM and Pegan SD (2014) Structural and functional characterization of methicillin-resistant Staphylococcus aureus's class IIb fructose 1,6-bisphosphate aldolase. Biochemistry 53, 7604-7614 https://doi.org/10.1021/bi501141t
  15. Lee SJ, Jang JH, Yoon GY et al (2016) Mycobacterium abscessus D-alanyl-D-alanine dipeptidase induces the maturation of dendritic cells and promotes Th1-biased immunity. BMB Rep 49, 554-559 https://doi.org/10.5483/BMBRep.2016.49.10.080
  16. Kim JH, Choi JS, Kim S et al (2015) Synergistic effect of two E2 ubiquitin conjugating enzymes in SCF(hFBH1) catalyzed polyubiquitination. BMB Rep 48, 25-29 https://doi.org/10.5483/BMBRep.2015.48.1.057
  17. Winn MD, Ballard CC, Cowtan KD et al (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67, 235-242 https://doi.org/10.1107/S0907444910045749
  18. Emsley P, Lohkamp B, Scott WG and Cowtan K (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66, 486-501 https://doi.org/10.1107/S0907444910007493
  19. Murshudov GN, Skubak P, Lebedev AA et al (2011) REFMAC5 for the refinement of macromolecular crystal structures Acta Crystallogr D Biol Crystallogr 67, 355-367 https://doi.org/10.1107/S0907444911001314
  20. Afonine PV, Grosse-Kunstleve RW, Echols N et al (2012) Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr 68, 352-367
  21. Laskowski R, MacArthur M, Moss D and Thornton J (1993) PROCHECK: A program to check the stereochemical quality of protein structures. J Appl Cryst 26, 283-291 https://doi.org/10.1107/S0021889892009944
  22. Krissinel E (2012) Enhanced fold recognition using efficient short fragment clustering. J Mol Biochem 1, 76-85
  23. Schrodinger L (2010) The PyMOL Molecular Graphics System, Version 1.3r1.
  24. Notredame C, Higgins DG and Heringa J (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302, 205-217 https://doi.org/10.1006/jmbi.2000.4042
  25. Gouet P CESD and Metoz F (1999) ESPript: multiple sequence alignments in PostScript. Bioinformatic 15, 305-308 https://doi.org/10.1093/bioinformatics/15.4.305