Enzyme-Dependent [4 + 2] Cycloaddition Depends on Lid-like Interaction of the N-Terminal Sequence with the Catalytic Core in PyrI4

Cell Chemical Biology

Volumn 23, Issue 3, 2016, Pages 352-360

  Zheng, Qingfei ^a   Guo, Yujiao ^a   Yang, Linlin ^b   Zhao, Zhixiong ^a   Wu, Zhuhua ^a   Zhang, Hua ^a   Liu, Jianping ^a   Cheng, Xiaofang ^a   Wu, Jiequn ^a,c   Yang, Huaiyu ^b   Jiang, Hualiang ^b   Pan, Lifeng ^a   Liu, Wen ^a,c  

^a SHANGHAI INSTITUTE OF ORGANIC CHEMISTRY   (China)

^b SHANGHAI INSTITUTE OF MATERIA MEDICA   (China)

^c Huzhou Center of Bio Synthetic Innovation   (China)

Author keywords

[No Author keywords available]

Indexed keywords

PYRI4 ENZYME; SYNTHETASE; UNCLASSIFIED DRUG; MACROLIDE; PEPTIDE SYNTHASE; SPIRO COMPOUND;

AMINO TERMINAL SEQUENCE; ARTICLE; BIOCHEMICAL ANALYSIS; BIOSYNTHESIS; CATALYSIS; COMPLEX FORMATION; CONJUGATION; CRYSTAL STRUCTURE; CRYSTALLIZATION; CYCLIZATION; CYCLOADDITION; DIELS ALDER REACTION; ENZYME ACTIVITY; ENZYME CONFORMATION; MOLECULAR INTERACTION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; STREPTOMYCES; STREPTOMYCES RUGOSPORUS; AMINO ACID SEQUENCE; BIOCATALYSIS; CHEMISTRY; METABOLISM; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; BIOCATALYSIS; CYCLOADDITION REACTION; MACROLIDES; MOLECULAR DYNAMICS SIMULATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PEPTIDE SYNTHASES; SEQUENCE ALIGNMENT; SPIRO COMPOUNDS;

EID: 84965159401     PISSN: 24519456     EISSN: 24519448     Source Type: Journal    
DOI: 10.1016/j.chembiol.2016.01.005     Document Type: Article

References (33)

1. P.D. Adams, R.W. Grosse-Kunstleve, L.W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.J. Read, J.C. Sacchettini, N.K. Sauter, and T.C. Terwilliger PHENIX: building new software for automated crystallographic structure determination Acta Crystallogr. D Biol. Crystallogr. 58 2002 1948 1954
2. A. Bax, and S. Grzesiek Methodological advances in protein NMR Acc. Chem. Res. 26 1993 131 138
3. I.W. Davis, A. Leaver-Fay, V.B. Chen, J.N. Block, G.J. Kapral, X. Wang, L.W. Murray, W.B. Arendall 3rd, J. Snoeyink, J.S. Richardson, and et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids Nucleic Acids Res. 35 2007 W375 W383
4. F. Delaglio, S. Grzesiek, G.W. Vuister, G. Zhu, J. Pfeifer, and A. Bax NMRPipe-a multidimensional spectral processing system based on UNIX pipes J. Biomol. NMR 6 1995 277 293
5. W. Ding, D.R. Williams, P. Northcote, M.M. Siegel, R. Tsao, J. Ashcroft, G.O. Morton, M. Alluri, D. Abbanat, W.M. Maiese, and et al. Pyrroindomycins, novel antibiotics produced by Streptomyces rugosporus sp. LL-42D005. I. Isolation and structure determination J. Antibiot. 47 1994 1250 1257
6. H. Du, and K. Ding Asymmetric catalysis of Diels-Alder reaction S. Ma, Handbook of Cyclization Reactions 2010 Wiley-VCH Verlag 1 57
7. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr. D Biol. Crystallogr. 60 2004 2126 2132
8. C.D. Fage, E.A. Isiorho, Y. Liu, D.T. Wagner, H.-w. Liu, and A.T. Keatinge-Clay The structure of SpnF, a standalone enzyme that catalyzes [4+2] cycloaddition Nat. Chem. Biol. 11 2015 256 258
9. R.A. Friesner, J.L. Banks, R.B. Murphy, T.A. Halgren, J.J. Klicic, D.T. Mainz, M.P. Repasky, E.H. Knoll, M. Shelley, J.K. Perry, and et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy J. Med. Chem. 47 2004 1739 1749
10. V.E. Gouverneur, K.N. Houk, B. de Pascual-Teresa, B. Beno, K.D. Janda, and R.A. Lerner Control of the exo and endo pathways of the Diels-Alder reaction by antibody catalysis Science 262 1993 204 208
11. M.R. Green, and J. Sambrook Molecular Cloning: a Laboratory Manual Fourth Edition 2012 Cold Spring Harbor Laboratory Press
12. T. Hashimoto, J. Hashimoto, K. Teruya, T. Hirano, K. Shin-ya, H. Ikeda, H.-w. Liu, M. Nishiyama, and T. Kuzuyama Biosynthesis of versipelostatin: identification of an enzyme-catalyzed [4+2]-cycloaddition required for macrocyclization of spirotetronate-containing polyketides J. Am. Chem. Soc. 137 2015 572 575
13. X. Jia, Z. Tian, L. Shao, X. Qu, Q. Zhao, J. Tang, G. Tang, and W. Liu Genetic characterization of the chlorothricin gene cluster as a model for spirotetronate antibiotic biosynthesis Chem. Biol. 13 2006 575 585
14. H.J. Kim, M.W. Ruszczycky, S.H. Choi, Y.N. Liu, and H.-W. Liu Enzyme-catalysed [4+2] cycloaddition is a key step in the biosynthesis of spinosyn A Nature 473 2011 109 112
15. H.J. Kim, M.W. Ruszczycky, and H.-W. Liu Current developments and challenges in the search for a naturally selected Diels-Alderase Curr. Opin. Chem. Biol. 16 2012 124 131
16. K. Klas, S. Tsukamoto, D.H. Sherman, and R.M. Williams Natural Diels-Alderases: elusive and irresistible J. Org. Chem. 80 2015 11672 11685
17. M.H. Lacoske, and E.A. Theodorakis Spirotetronate polyketides as leads in drug discovery J. Nat. Prod. 78 2015 562 575
18. G.N. Murshudov, A.A. Vagin, and E.J. Dodson Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallogr. D Biol. Crystallogr. 53 1997 240 255
19. P. Neumann, F. Brodhun, K. Sauer, C. Herrfurth, M. Hamberg, J. Brinkmann, J. Scholz, A. Dickmanns, I. Feussner, and R. Ficner Crystal structures of Physcomitrella patens AOC1 and AOC2: insights into the enzyme mechanism and differences in substrate specificity Plant Physiol. 160 2012 1251 1266
20. H. Oikawa, and T. Tokiwano Enzymatic catalysis of the Diels-Alder reaction in the biosynthesis of natural products Nat. Prod. Rep. 21 2004 321 352
21. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326
22. B. Pang, M. Wang, and W. Liu Cyclization of polyketides and non-ribosomal peptides on and off their assembly lines Nat. Prod. Rep. 2016 10.1039/C5NP00095E
23. Schrödinger LigPrep, Version 2.5 2011 Schrödinger LLC
24. B. Seelig, and A. Jäschke A small catalytic RNA motif with Diels-Alderase activity Chem. Biol. 6 1999 167 176
25. J.B. Siegel, A. Zanghellini, H.M. Lovick, G. Kiss, A.R. Lambert, J.L. St Clair, J.L. Gallaher, D. Hilvert, M.H. Gelb, B.L. Stoddard, and et al. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction Science 329 2010 309 313
26. M.P. Singh, P.J. Petersen, N.V. Jacobus, M.J. Mroczenski-Wildey, W.M. Maiese, M. Greenstein, and D.A. Steinberg Pyrroindomycins, novel antibiotics produced by Streptomyces rugosporus LL-42D005. II. Biological activities J. Antibiot. 47 1994 1258 1265
27. L.C. Storoni, A.J. McCoy, and R.J. Read Likelihood-enhanced fast rotation functions Acta Crystallogr. D Biol. Crystallogr. 60 2004 432 438
28. T.C. Terwilliger, P.D. Adams, R.J. Read, A.J. McCoy, N.W. Moriarty, R.W. Grosse-Kunstleve, P.V. Afonine, P.H. Zwart, and L.W. Hung Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard Acta Crystallogr. D Biol. Crystallogr. 65 2009 582 601
29. Z. Tian, P. Sun, Y. Yan, Z. Wu, Q. Zheng, S. Zhou, H. Zhang, F. Yu, X. Jia, D. Chen, and et al. An enzymatic [4+2] cyclization cascade creates the pentacyclic core of pyrroindomycins Nat. Chem. Biol. 11 2015 259 265
30. Q. Wu, Z. Wu, X. Qu, and W. Liu Insights into pyrroindomycin biosynthesis reveal a uniform paradigm for tetramate/tetronate formation J. Am. Chem. Soc. 134 2012 17342 17345
31. K. Wuthrich NMR of Proteins and Nucleic Acids 1986 Wiley-Interscience
32. T. Yamaguchi, K. Saito, T. Tsujimoto, and H. Yuki NMR spectroscopic studies on the tautomerism in tenuazonic acid analogs J. Heterocycl. Chem. 13 1976 533 537
33. Q. Zheng, Z. Tian, and W. Liu Recent advances in understanding the enzymatic reactions of [4+2] cycloaddition and spiroketalization Curr. Opin. Chem. Biol. 31 2016 10.1016/j.cbpa.2016.01.020