Identification of biochemical and putative biological role of a xenolog from Escherichia coli using structural analysis
Varun Bhaskar
Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India
Search for more papers by this authorManoj Kumar
Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India
Search for more papers by this authorSankar Manicka
Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India
Search for more papers by this authorSunil Tripathi
Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India
Search for more papers by this authorAparna Venkatraman
Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India
Search for more papers by this authorCorresponding Author
S. Krishnaswamy
Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India
Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India===Search for more papers by this authorVarun Bhaskar
Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India
Search for more papers by this authorManoj Kumar
Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India
Search for more papers by this authorSankar Manicka
Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India
Search for more papers by this authorSunil Tripathi
Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India
Search for more papers by this authorAparna Venkatraman
Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India
Search for more papers by this authorCorresponding Author
S. Krishnaswamy
Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India
Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India===Search for more papers by this authorAbstract
YagE is a 33 kDa prophage protein encoded by CP4-6 prophage element in Escherichia coli K12 genome. Here, we report the structures of YagE complexes with pyruvate (PDB Id 3N2X) and KDGal (2-keto-3-deoxy galactonate) (PDB Id 3NEV) at 2.2Å resolution. Pyruvate depletion assay in presence of glyceraldehyde shows that YagE catalyses the aldol condensation of pyruvate and glyceraldehyde. Our results indicate that the biochemical function of YagE is that of a 2-keto-3-deoxy gluconate (KDG) aldolase. Interestingly, E. coli K12 genome lacks an intrinsic KDG aldolase. Moreover, the over-expression of YagE increases cell viability in the presence of certain bactericidal antibiotics, indicating a putative biological role of YagE as a prophage encoded virulence factor enabling the survival of bacteria in the presence of certain antibiotics. The analysis implies a possible mechanism of antibiotic resistance conferred by the over-expression of prophage encoded YagE to E. coli. Proteins 2011, © 2011 Wiley-Liss, Inc.
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REFERENCES
- 1 Casjens S. Prophages and bacterial genomics: what have we learned so far? Mol Microbiol 2003; 49: 277–300.
- 2 Joerger AC,Mayer S,Fersht AR. Mimicking natural evolution in vitro: an N-acetylneuraminate lyase mutant with an increased dihydrodipicolinate synthase activity. Proc Natl Acad Sci USA 2003; 100: 5694–5699.
- 3 Barbosa JA,Smith BJ,DeGori R,Ooi HC,Marcuccio SM,Campi EM,Jackson WR,Brossmer R,Sommer M,Lawrence MC. Active site modulation in the N-acetylneuraminate lyase sub-family as revealed by the structure of the inhibitor-complexed Haemophilus influenzae enzyme. J Mol Biol 2000; 303: 405–421.
- 4 Laber B,Gomis-Ruth FX,Romao MJ,Huber R. Escherichia coli dihydrodipicolinate synthase. Identification of the active site and crystallization. Biochem J 1992; 288 (Part 2): 691–695.
- 5 Lawrence MC,Barbosa JA,Smith BJ,Hall NE,Pilling PA,Ooi HC,Marcuccio SM. Structure and mechanism of a sub-family of enzymes related to N-acetylneuraminate lyase. J Mol Biol 1997; 266: 381–399.
- 6 Blickling S,Renner C,Laber B,Pohlenz HD,Holak TA,Huber R. Reaction mechanism of Escherichia coli dihydrodipicolinate synthase investigated by X-ray crystallography and NMR spectroscopy. Biochemistry 1997; 36: 24–33.
- 7 Dobson RC,Valegard K,Gerrard JA. The crystal structure of three site-directed mutants of Escherichia coli dihydrodipicolinate synthase: further evidence for a catalytic triad. J Mol Biol 2004; 338: 329–339.
- 8 Blattner FR,Plunkett G,III,Bloch CA,Perna NT,Burland V,Riley M,Collado-Vides J,Glasner JD,Rode CK,Mayhew GF,Gregor J,Davis NW,Kirkpatrick HA,Goeden MA,Rose DJ,Mau B,Shao Y. The complete genome sequence of Escherichia coli K-12. Science 1997; 277: 1453–1462.
- 9 Manicka S,Peleg Y,Unger T,Albeck S,Dym O,Greenblatt HM,Bourenkov G,Lamzin V,Krishnaswamy S,Sussman JL. Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12. Proteins 2008; 71: 2102–2108.
- 10 Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J Appl crystallography 1993; 26: 795–800.
- 11 McCoy AJ,Grosse-Kunstleve RW,Adams PD,Winn MD,Storoni LC,Read RJ. Phaser crystallographic software. J Appl Crystallogr 2007; 40: 658–674.
- 12 Murshudov GN,Vagin AA,Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 1997; 53: 240–255.
- 13 Vagin AA,Steiner RA,Lebedev AA,Potterton L,McNicholas S,Long F,Murshudov GN. REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. Acta Crystallogr D Biol Crystallogr 2004; 60: 2184–2195.
- 14 Adams PD,Afonine PV,Bunkóczi G,Chen VB,Davis IW,Echols N,Headd JJ,Hung LW,Kapral GJ,Grosse-Kunstleve RW,McCoy AJ,Moriarty NW,Oeffner R,Read RJ,Richardson DC,Richardson JS,Terwilliger TC,Zwart PH. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst 2010; D66: 213–221.
- 15 Emsley P,Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 2004; 60: 2126–2132.
- 16 CCP4Team. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 1994; 50: 760–763.
- 17 Friesner RA,Banks JL,Murphy RB,Halgren TA,Klicic JJ,Mainz DT,Repasky MP,Knoll EH,Shelley M,Perry JK,Shaw DE,Francis P,Shenkin PS. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004; 47: 1739–1749.
- 18 Halgren TA,Murphy RB,Friesner RA,Beard HS,Frye LL,Pollard WT,Banks JL. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 2004; 47: 1750–1759.
- 19 Verdonk ML,Cole JC,Hartshorn MJ,Murray CW,Taylor RD. Improved protein-ligand docking using GOLD. Proteins 2003; 52: 609–623.
- 20 Garrett MM,Ruth H,William L,Michel FS,Richard KB,David SG,Arthur JO. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 2002; 30: 2785–2791.
- 21 Theodossis A,Walden H,Westwick EJ,Connaris H,Lamble HJ,Hough DW,Danson MJ,Taylor GL. The structural basis for substrate promiscuity in 2-keto-3-deoxygluconate aldolase from the Entner-Doudoroff pathway in Sulfolobus solfataricus. J Biol Chem 2004; 279: 43886–43892.
- 22 Pearce FG,Perugini MA,McKerchar HJ,Gerrard JA. Dihydrodipicolinate synthase from Thermotoga maritima. Biochem J 2006; 400: 359–366.
- 23 Delano WL. The PyMOL molecular graphics system. DeLano Scientific, San Carlos, CA, USA, 2002.
- 24 Pettersen EF,Goddard TD,Huang CC,Couch GS,Greenblatt DM,Meng EC,Ferrin TE. UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem 2004; 25: 1605–1612.
- 25 Comb DG,Roseman S. The sialic acids. I. The structure and enzymatic synthesis of N-acetylneuraminic acid. J Biol Chem 1960; 235: 2529–2537.
- 26 Wolterink-Van Loo S,Andr'e Van E,Marco AJS,Jasper A,Bauke WD,Van Der Oost J. Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases. Biochem J 2007; 403: 421–430.
- 27 Yugari Y,Gilvarg C. The condensation step in diaminopimelate synthesis. J Biol Chem 1965; 240: 4710–4716.
- 28 Dobson RC,Devenish SR,Turner LA,Clifford VR,Pearce FG,Jameson GB,Gerrard JA. Role of arginine 138 in the catalysis and regulation of Escherichia coli dihydrodipicolinate synthase. Biochemistry 2005; 44: 13007–13013.
- 29 Borthwick EB,Connell SJ,Tudor DW,Robins DJ,Shneier A,Abell C,Coggins JR. Escherichia coli dihydrodipicolinate synthase: characterization of the imine intermediate and the product of bromopyruvate treatment by electrospray mass spectrometry. Biochem J 1995; 305 (Part 2): 521–524.
- 30 Michael AK,Daniel JD,Boris H,Carolyn AL,James JC. A common mechanism of cellular death induced by bactericidal antibiotics. Cell 2007; 130: 797–810.
- 31 Kenneth ER. EcoGene: a genome sequence database for Escherichia coli K-12. NAR 2000; 28: 60–64.
- 32 Harry GB. Solid-state fluorescence of the trihydrate phases of ampicillin and amoxicillin. AAPS PharmSciTech 2005; 6: 444–448.
- 33 Gongwu S,Yu H,Zhaoxia C. A fluorescence spectroscopic study of the interaction between norfloxacin and DNA. Can J Anal Sci Spectroscopy 2004; 49: 203–209.
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