Probing the determinants of phosphorylated sugar-substrate binding for human sialic acid synthase

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1844, Issue 12, 2014, Pages 2257-2264

  Cotton, Thomas R ^a   Joseph, Dmitri D A ^a   Jiao, Wanting ^a   Parker, Emily J ^a  

^a UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

Homo sapiens; Homology model; N acetylmannosamine 6 phosphate; N acetylneuraminic acid; Substrate selectivity

Indexed keywords

ALANINE; ENZYME; HOMODIMER; LYSINE; PHOSPHATE; SIALIC ACID; SUGAR;

ARTICLE; CATALYSIS; ENZYME SPECIFICITY; ENZYME SUBSTRATE; ISOTHERMAL TITRATION CALORIMETRY; MAMMAL; MUTAGENESIS; NONHUMAN; PROTEIN PHOSPHORYLATION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SUBSTITUTION REACTION; X RAY CRYSTALLOGRAPHY;

EID: 84908192680     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2014.09.014     Document Type: Article

References (39)

1. M.E. Tanner The enzymes of sialic acid biosynthesis Bioorg. Chem. 33 2005 216 228
2. C. Traving, and R. Schauer Structure, function and metabolism of sialic acids Cell. Mol. Life Sci. 54 1998 1330 1349
3. J.J. Hao, P. Balagurumoorthy, S. Suryakala, and M. Sundaramoorthy Cloning, expression, and characterization of sialic acid synthases Biochem. Biophys. Res. Commun. 338 2005 1507 1514
4. R. Schauer Sialic acids: fascinating sugars in higher animals and man Zoology (Jena) 107 2004 49 64
5. F. Liu, H.J. Lee, N.C.J. Strynadka, and M.E. Tanner Inhibition of Neisseria meningitidis sialic acid synthase by a tetrahedral intermediate analogue Biochemistry 48 2009 9194 9201
6. E. Severi, D.W. Hood, and G.H. Thomas Sialic acid utilization by bacterial pathogens Microbiology 153 2007 2817 2822
7. E.R. Vimr, K.A. Kalivoda, E.L. Deszo, and S.M. Steenbergen Diversity of microbial sialic acid metabolism Microbiol. Mol. Biol. Rev. 68 2004 132 153
8. J. Gunawan, D. Simard, M. Gilbert, A.L. Lovering, W.W. Wakarchuk, M.E. Tanner, and N.C.J. Strynadka Structural and mechanistic analysis of sialic acid synthase NeuB from Neisseria meningitidis in complex with Mn2 + phosphoenolpyruvate, and N-acetylmannosaminitol J. Biol. Chem. 280 2005 3555 3563
9. R.S. Blacklow, and L. Warren Biosynthesis of sialic acids by Neisseria meningitidis J. Biol. Chem. 237 1962 3520 3526
10. H. Chen, A. Blume, M. Zimmermann-Kordmann, W. Reutter, and S. Hinderlich Purification and characterization of N-acetylneuraminic acid-9-phosphate synthase from rat liver Glycobiology 12 2002 65 71
11. S. Roseman, R. Rood, D. Watson, and G.W. Jourdian Enzymatic synthesis of sialic acid 9-phosphates Proc. Natl. Acad. Sci. U. S. A. 47 1961 958 961
12. I.G. Bravo, S. García-Vallvé, A. Romeu, and A. Reglero Prokaryotic origin of cytidylyltransferases and α-ketoacid synthases Trends Microbiol. 12 2004 120 128
13. W.K. Chou, S. Dick, W.W. Wakarchuk, and M.E. Tanner Identification and characterization of NeuB3 from Campylobacter jejuni as a pseudaminic acid synthase J. Biol. Chem. 280 2005 35922 35928
14. D. Linton, A.V. Karlyshev, P.G. Hitchen, H.R. Morris, A. Dell, N.A. Gregson, and B.W. Wren Multiple N-acetyl neuraminic acid synthetase (neuB) genes in Campylobacter jejuni: identification and characterization of the gene involved in sialylation of lipo-oligosaccharide Mol. Microbiol. 35 2000 1120 1134
15. I.C. Schoenhofen, E. Vinogradov, D.M. Whitfield, J.-R. Brisson, and S.M. Logan The CMP-legionaminic acid pathway in Campylobacter: biosynthesis involving novel GDP-linked precursors Glycobiology 19 2009 715 725
16. I.C. Schoenhofen, D.J. McNally, J.-R. Brisson, and S.M. Logan Elucidation of the CMP-pseudaminic acid pathway in Helicobacter pylori: synthesis from UDP-N-acetylglucosamine by a single enzymatic reaction Glycobiology 16 2006 8C 14C
17. A.K. Sundaram, L. Pitts, K. Muhammad, J. Wu, M. Betenbaugh, R.W. Woodard, and W.F. Vann Characterization of N-acetylneuraminic acid synthase isoenzyme 1 from Campylobacter jejuni Biochem. J. 383 2004 83 89
18. J. Baardsnes, and P.L. Davies Sialic acid synthase: the origin of fish type III antifreeze protein? Trends Biochem. Sci. 26 2001 468 469
19. D.D.A. Joseph, W. Jiao, and E.J. Parker Arg314 is essential for catalysis by N-acetyl neuraminic acid synthase from Neisseria meningitidis Biochemistry 52 2013 2609 2619
20. D.D.A. Joseph, W. Jiao, S.A. Kessans, and E.J. Parker Substrate-mediated control of the conformation of an ancillary domain delivers a competent catalytic site for N-acetylneuraminic acid synthase Proteins Struct. Funct. Bioinform. 2014 10.1002/prot.24558
21. S.M. Lawrence, K.A. Huddleston, L.R. Pitts, N. Nguyen, Y.C. Lee, W.F. Vann, T.A. Coleman, and M.J. Betenbaugh Cloning and expression of the human N-acetylneuraminic acid phosphate synthase gene with 2-keto-3-deoxy-d-glycero-d-galacto-nononic acid biosynthetic ability J. Biol. Chem. 275 2000 17869 17877
22. J. Hao, W.F. Vann, S. Hinderlich, and M. Sundaramoorthy Elimination of 2-keto-3-deoxy-d-glycero-d-galacto-nonulosonic acid 9-phosphate synthase activity from human N-acetylneuraminic acid 9-phosphate synthase by a single mutation Biochem. J. 397 2006 195 201
23. T. Hamada, Y. Ito, T. Abe, F. Hayashi, P. Guntert, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, M. Yoshida, A. Tanaka, S. Sugano, S. Yokoyama, and H. Hirota Solution structure of the antifreeze-like domain of human sialic acid synthase Protein Sci. 15 2006 1010 1016
24. F. Sievers, A. Wilm, D. Dineen, T.J. Gibson, K. Karplus, W. Li, R. Lopez, H. McWilliam, M. Remmert, J. Soding, J.D. Thompson, and D.G. Higgins Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega Mol. Syst. Biol. 7 2011 539
25. M. Goujon, H. McWilliam, W. Li, F. Valentin, S. Squizzato, J. Paern, and R. Lopez A new bioinformatics analysis tools framework at EMBL-EBI Nucleic Acids Res. 38 2010 W695 W699
26. A.M. Waterhouse, J.B. Procter, D.M.A. Martin, M. Clamp, and G.J. Barton Jalview Version 2 - a multiple sequence alignment editor and analysis workbench Bioinformatics 25 2009 1189 1191
27. M.P. Jacobson, R.A. Friesner, Z.X. Xiang, and B. Honig On the role of the crystal environment in determining protein side-chain conformations J. Mol. Biol. 320 2002 597 608
28. M.P. Jacobson, D.L. Pincus, C.S. Rapp, T.J.F. Day, B. Honig, D.E. Shaw, and R.A. Friesner A hierarchical approach to all-atom protein loop prediction Proteins Struct. Funct. Bioinform. 55 2004 351 367
29. Suite 2012: Prime, version 3.1 2012 Schrödinger, LLC New York, NY
30. Suite 2012: Maestro, version 9.3 2012 Schrödinger, LLC New York, NY
31. Suite 2012: LigPrep, version 2.5 2012 Schrödinger, LLC New York, NY
32. W. Sherman, T. Day, M.P. Jacobson, R.A. Friesner, and R. Farid Novel procedure for modeling ligand/receptor induced fit effects J. Med. Chem. 49 2005 534 553
33. R. Farid, T. Day, R.A. Friesner, and R.A. Pearlstein New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies Bioorg. Med. Chem. 14 2006 3160 3173
34. W. Sherman, H.S. Beard, and R. Farid Use of an induced fit receptor structure in virtual screening Chem. Biol. Drug Des. 67 2006 83 84
35. Suite 2012: Schrödinger Suite Induced fit docking protocol 2012
36. P.V. Konarev, V.V. Volkov, A.V. Sokolova, M.H.J. Koch, and D.I. Svergun PRIMUS: a Windows PC-based system for small-angle scattering data analysis J. Appl. Crystallogr. 36 2003 1277 1282
37. D. Svergun, C. Barberato, and M.H.J. Koch CRYSOL - a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates J. Appl. Crystallogr. 28 1995 768 773
38. M.L. Reaves, L.C. Lopez, and S.M. Daskalova Replacement of the antifreeze-like domain of human N-acetylneuraminic acid phosphate synthase with the mouse antifreeze-like domain impacts both N-acetylneuraminic acid 9-phosphate synthase and 2-keto-3-deoxy-d-glycero-d-galacto-nonulosonic acid 9-phosphate synthase activities BMB Rep. 41 2008 72 78
39. S. Reichau, W. Jiao, S.R. Walker, R.D. Hutton, E.N. Baker, and E.J. Parker Potent inhibitors of a shikimate pathway enzyme from Mycobacterium tuberculosis - combining mechanism- and modeling-based design J. Biol. Chem. 286 2011 16197 16207