Undecaprenyl diphosphate synthase, a cis-prenyltransferase synthesizing lipid carrier for bacterial cell wall biosynthesis

Molecular Membrane Biology

Volumn 29, Issue 7, 2012, Pages 267-273

  Teng, Kuo Hsun ^a   Liang, Po Huang ^a  

^a INSTITUTE OF BIOLOGICAL CHEMISTRY   (Taiwan)

Author keywords

Conformational change; Inhibitor; Isoprenoid; Mechanism; Pre steady state kinetics; Prenyltransferase

Indexed keywords

BISPHOSPHONIC ACID DERIVATIVE; DIHYDROPYRIDIN 2 ONE; DIMETHYLALLYLTRANSFERASE; ISOPENTENYL DIPHOSPHATE; TETRAMIC ACID DERIVATIVE; TETRONIC ACID DERIVATIVE; TRANSFERASE INHIBITOR; UNCLASSIFIED DRUG; UNDECAPRENYLDIPHOSPHATE SYNTHASE;

BACTERIAL CELL WALL; BIOSYNTHESIS; CATALYSIS; CONFORMATIONAL TRANSITION; DRUG SCREENING; ENZYME INHIBITION; ENZYME KINETICS; ENZYME STRUCTURE; ENZYME SYNTHESIS; HUMAN; NONHUMAN; POLYMERIZATION; PRIORITY JOURNAL; PROTEIN FUNCTION; REVIEW;

ALKYL AND ARYL TRANSFERASES; BACTERIA; BACTERIAL PROTEINS; CELL WALL; DIMETHYLALLYLTRANSTRANSFERASE; HEMITERPENES; ORGANOPHOSPHORUS COMPOUNDS; POLYISOPRENYL PHOSPHATES; PROTEIN STRUCTURE, TERTIARY; SESQUITERPENES; STRUCTURE-ACTIVITY RELATIONSHIP;

BACTERIA (MICROORGANISMS);

EID: 84867972691     PISSN: 09687688     EISSN: 14645203     Source Type: Journal    
DOI: 10.3109/09687688.2012.674162     Document Type: Review

References (37)

1. Allen CM. 1985. Purification and characterization of undecaprenyl pyrophosphate synthase. Methods Enzymol 110:281-299.
2. Bamba T, Fukusaki E, Kajiyama S, Ute K, Kitayama T, Kobayashi A. 2001. The occurrence of geometric polyprenol isomers in the rubber-producing plant, Eucommia ulmoides Oliver. Lipids 36:727-736.
3. Bloch K, Chaykin S, Phillips AH, de Waard A. 1959. Mevalonic acid pyrophosphate and isopentenyl pyrophosphate. J Biol Chem 234:2595-2608.
4. Chang SY, Ko TP, Liang PH, Wang AHJ. 2003a. Catalytic mechanism revealed by the crystal structure of undecaprenyl pyrophosphate synthase in complex with sulfate, magnesium, and Triton. J Biol Chem 278:29298-29307.
5. Chang SY, Chen YK, Wang AHJ, Liang PH. 2003b. Identification of the active conformation and the importance of length of the flexible loop in regulating conformational change in undecaprenyl pyrophosphate synthase. Biochemistry 42:14452-14459.
6. Chang SY, Ko TP, Chen APC, Wang AHJ, Liang PH. 2004. Substrate binding mode and reaction mechanism of undecaprenyl pyrophosphate synthase deduced from crystallographic studies. Protein Sci 13:971-978.
7. Chen APC, Chen YH, Liu HP, Li YC, Chen CT, Liang PH. 2002. Application of synthetic fluorescent substrate analogues to study ligand interactions for undecaprenyl pyrophosphate synthase. J Am Chem Soc 124:15217-15224.
8. Chen APC, Chang SY, Lin YC, Sun YS, Chen CT, Wang AHJ, et al. 2005. Substrate and product specificities of cis-type undecaprenyl pyrophosphate synthase. Biochem J 386:169-176.
9. Chen CK, Hudock MP, Zhang Y, Kuo RT, Cao R, No JH, et al. 2008. Inhibition of geranylgeranyl diphosphate synthase by bisphosphonates: A crystallographic and computational Investigation. J Med Chem 51:5594-5607.
10. Chen YH, Chen APC, Chen CT, Wang AHJ, Liang PH. 2002. Probing the conformational change of E. coli undecaprenyl pyrophosphate synthase during catalysis using an inhibitor and tryptophan mutants. J Biol Chem 277:7369-7376.
11. Cornish K. 1993. The separate roles of plant cis and trans prenyl transferases in cis-1,4-polyisoprene biosynthesis. Eur J Biochem 218:267-271. (Pubitemid 23350383)
12. Durbecq V, Sainz S, Oudjama Y, Clantin B, Bompard-Gilles C, Tricot C, et al. 2001.Crystal structure of isopentenyl diphosphate: dimethylally diphosphate isomerase. EMBO J 20:1530-1537. (Pubitemid 32299390)
13. Fujihashi M, Zhang YW, Higuchi Y, Li XY, Koyama T, Miki K. 2001. Crystal structure of cis-prenyl chain elongating enzyme, undecaprenyl diphosphate synthase. Proc Natl Acad Sci USA 98:4337-4442.
14. Guo RT, Ko TP, Chen APC, Kuo CJ, Wang AHJ, Liang PH. 2005. Crystal structures of undecaprenyl pyrophosphate synthase in complex with magnesium, isopentenyl pyrophosphate and farnesyl thiopyrophosphate: roles of the metal ion and conserved residues in catalysis. J Biol Chem 280:20762-20774.
15. Guo RT, Cao R, Liang PH, Chang TH, Ko TP, Jeng WY, et al. 2007. Bisphosphonates target multiple sites in both cis-and trans-prenyltransferases. a. crystallographic investigation. Proc Natl Acad Sci USA 104:10022-10027. (Pubitemid 47175256)
16. Hosfield DJ, Zhang Y, Dougan DR, Broun A, Tari LW, Swanson RV, et al. 2004. Structural basis for bishosphontaemediated inhibition of isoprenoid biosynthesis. J Biol Chem 279:8526-8529. (Pubitemid 38295905)
17. Ko TP, Chen YK, Robinson H, Tsai PC, Gao YG, Chen APC, et al. 2001. Mechanism of the product chain length determination and the role of a flexible loop in E. coli undecaprenyl pyrophosphate synthase catalysis. J Biol Chem 276:47474-47482.
18. Kuo CJ, Guo RT, Lu IL, Liu HG, Wu SY, Ko TP, et al. 2008. Structure-based inhibitors exhibited differential activities against H. pylori and E. coli undecaprenyl pyrophosphate synthases. J Biomed Biotechnol 841312.
19. Lee LV, Granda B, Dean K, Tao J, Liu E, Zhang R, et al. 2010. Biophysical investigation of the mode of inhibition of tetramic acids, the allosteric inhibiors of undecaprenyl pyrophosphate synthase. Biochemistry 49:5366-5376.
20. Li H, Huang J, Jiang X, Seefeld M, McQuenery M, Macarron R. 2003. The effect of Triton concentration on the activity of undecaprenyl pyrophosphate synthase activity. J Biomol Screen 8:712-715.
21. Liang PH, Ko TP, Wang AHJ. 2002. Structure, mechanism and function of prenyltransferases. Eur J Biochem 269:3339-3354.
22. Liang PH. 2009. Reaction kinetics, catalytic mechanisms, conformational changes, and inhibitor design for prenyltransferases. Biochemistry 48:6562-6570.
23. Lu YP, Liu HG, Liang PH. 2009. Different reaction mechanisms for cis-and trans-prenyltransferases. Biochem Biophys Res Commun 379:351-355.
24. Lu YP, Liu HG, Teng KH, Liang PH. 2010. Mechanism of cis- prenyltransferase reaction probed by substrate analogues. Biophys Biochem Res Commun 400:758-762.
25. Ogura K, Koyama T. 1998. Enzymatic aspects of isoprenoid chain elongation. Chem Rev 98:1263-1276.
26. Pan JJ, Chiou ST, Liang PH. 2000. Product distribution and pre-steady-state kinetic analysis of Escherichia coli undecaprenyl pyrophosphate synthase reaction. Biochemistry 39:10936-10942.
27. Peukert S, Sun Y, Zhang R, Hurley B, Sabio M, Shen X, et al. 2008. Design and structure-activity relationships of potent and selective inhibitors of undecaprenyl pyrophosphate synthase (UPPS): Tetramic, tetronic acids and dihydropyridine-2-ones. Bioorg Med Chem Lett 18:1840-1844. (Pubitemid 351380899)
28. Poulter CD, Argyle JC, Mash EA. 1977. Letter: Prenyltransferase. New evidence for an ionization-condensation-elimination mechanism with 2-fluorogeranyl pyrophosphate. J Am Chem Soc 99:957-959.
29. Poulter CD, Satterwhite DM. 1977. Mechanism of the prenyltransfer reaction: Studies with (E)-and (Z)-3-trifluoromethyl-2-buten-1-yl pyrophosphate. Biochemistry 16:5470-5478. (Pubitemid 8254137)
30. Poulter CD, Rilling HC. 1981. Biosynthesis of isoprenoid compounds. (Porter, J. W., and Spurgeon, S. L., eds.), Vol. 1, pp 161-224, John Wiley & Sons, New York.
31. Poznański J, Szkopinska A. 2007. Precise bacterial polyprenol length control fails in Saccharomyces cerevisiae. Biopolymers 86:155-164. (Pubitemid 46814988)
32. Rohmer M. 1999. The discovery of a mevalonate-independent pathway for isoprenoid biosynthesis in bacteria, algae, and higher plants. Nat Prot Rep 16:565-674.
33. Schulbach MC, Brennan PJ, Crick DC. 2000. Identification of a short (C15) chain Z-isoprenyl diphosphate synthase and a homologous long (C50) chain isoprenyl diphosphate synthase in Mycobacterium tuberculosis. J Biol Chem 275: 22876-22881. (Pubitemid 30646173)
34. Shimizu N, Koyama T, Ogura K. 1998. Molecular cloning, expression, and purification of undecaprenyl diphosphate synthase. J Biol Chem 273:19476-19481.
35. Sinko W, de Oliveria C, Williams S, Wynsberghe AV, Durrant JD, Cao R, et al. 2011. Applying molecular dynamics simulations to identify rarely sampled ligand-bound conformational states of undecaprenyl pyrophosphate synthase, an antibacterial target. Chem Biol Drug Des 7:412-420.
36. Teng KH, Chen APC, Kuo CJ, Li YC, Liu HG, Chen CT, et al. 2011. Fluorescent substrate analog for monitoring chain elongation by undecaprenyl pyrophosphate synthase in real time. Anal Biochem 417:136-141.
37. Upson RH, Haugland RP, Malekzadeh MN. 1996. A spectrophotometric method to measure enzymatic activity in reactions that generate inorganic pyrophosphate. Anal Biochem 243:41-45. (Pubitemid 26418574)