Role of protein conformational dynamics in the catalysis by 6-hydroxymethyl-7, 8-dihydropterin pyrophosphokinase

Protein and Peptide Letters

Volumn 18, Issue 4, 2011, Pages 328-335

  Yan, Honggao ^a   Ji, Xinhua ^b  

^a Michigan State University   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

6 hydroxymethyl 7; 8 dihydropterin pyrophosphokinase; Bisubstrate enzyme; Enzymatic catalysis; Folate biosynthesis; HPPK; NMR; Protein dynamics; X ray crystallography

Indexed keywords

2 AMINO 4 HYDROXY 6 HYDROXYMETHYLDIHYDROPTERIDINE PYROPHOSPHOKINASE; 2-AMINO-4-HYDROXY-6-HYDROXYMETHYLDIHYDROPTERIDINE PYROPHOSPHOKINASE; FOLIC ACID; PHOSPHOTRANSFERASE;

ARTICLE; BIOSYNTHESIS; CATALYSIS; CHEMISTRY; ENZYME SPECIFICITY; ENZYMOLOGY; ESCHERICHIA COLI; KINETICS; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

CATALYSIS; CRYSTALLOGRAPHY, X-RAY; DIPHOSPHOTRANSFERASES; ESCHERICHIA COLI; FOLIC ACID; KINETICS; MOLECULAR DYNAMICS SIMULATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; SUBSTRATE SPECIFICITY;

EID: 79951617237     PISSN: 09298665     EISSN: None     Source Type: Journal    
DOI: 10.2174/092986611794654003     Document Type: Article

References (28)

1. Hitchings, G.H.; Burchall, J.J. Inhibition of folate biosynthesis and function as a basis for chemotherapy. Adv. Enzymol. Relat. Areas Mol. Biol. 1965, 27, 417-468.
2. Walsh, C., Where will new antibiotics come from? Nat. Rev. Microbiol. 2003, 1, 65-70.
3. Bermingham, A.; Derrick, J.P. The folic acid biosynthesis pathway in bacteria: evaluation of potential for antibacterial drug discovery. Bioessays, 2002, 24, 637-648. (Pubitemid 34780351)
4. Zinner, S.H.; Mayer, K.H. Sulfonamides and trimethoprim. In Principles and Practice of Infectious Diseases, 6th ed.; Mandell, G. L.; Bennett, J. E.; Dolin, R. Eds. Churchill Livingstone: Philadelphia, 2005; Vol. 1, pp. 440-451.
5. Garçon, A.; Levy, C.; Derrick, J.P. Crystal structure of the bifunctional dihydroneopterin aldolase/6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase from Streptococcus pneumoniae. J. Mol. Biol., 2006, 360, 644-653. (Pubitemid 43977866)
6. Lawrence, M.C.; Iliades, P.; Fernley, R.T.; Berglez, J.; Pilling, P.A.; Macreadie, I.G. The three-dimensional structure of the bifunctional 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase/ dihydropteroate synthase of Saccharomyces cerevisiae. J. Mol. Biol., 2005, 348, 655-670. (Pubitemid 40515676)
7. Al Hassan, S.S.; Cameron, R.J.; Curran, A.W.C.; Lyall, W.J.S.; Nicholson, S.H.; Robinson, D.R.; Stuart, A.; Suckling, C.J.; Stirling, I.; Wood, H.C.S. Specific Inhibitors in Vitamin Biosynthesis .7. Syntheses of Blocked 7,8-Dihydropteridines Via Alpha-Amino Ketones. J. Chem. Soc.-Perkin Trans., 1 1985, 1645-1659.
8. Shi, G.; Blaszczyk, J.; Ji, X.; Yan, H. Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: Synthesis and biochemical and crystallographic studies. J. Med. Chem., 2001, 44, 1364-1371. (Pubitemid 32852112)
9. Wolfenden, R. Thermodynamic and extrathermodynamic requirements of enzyme catalysis. Biophys. Chem., 2003, 105, 559-572. (Pubitemid 37123084)
10. Bermingham, A.; Bottomley, J.R.; Primrose, W.U.; Derrick, J.P. Equilibrium and kinetic studies of substrate binding to 6-hydroxymethyl-7,8- dihydropterin pyrophosphokinase from Escherichia coli. J. Biol. Chem., 2000, 275, 17962-17967. (Pubitemid 30414740)
11. Li, Y.; Gong, Y.; Shi, G.; Blaszczyk, J.; Ji, X.; Yan, H. Chemical transformation is not rate-limiting in the reaction catalyzed by Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Biochemistry, 2002, 41, 8777-8783. (Pubitemid 34743319)
12. Xiao, B.; Shi, G.; Chen, X.; Yan, H.; Ji, X. Crystal structure of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, a potential target for the development of novel antimicrobial agents. Structure, 1999, 7, 489-496.
13. Neuhard, J.; Nygaard, P. Purines and pyrimidines. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, Neidhardt, F. C.; Ingraham, J. L.; Low, K. B.; Magasanik, B.; Schaechter, M.; Umbarger, H. E. Eds. ASM Press: Washington, D. C., 1987; Vol. 1, pp. 445-473.
14. Shi, G.; Gong, Y.; Savchenko, A.; Zeikus, J.G.; Xiao, B.; Ji, X.; Yan, H. Dissecting the nucleotide binding properties of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase with fluorescent 3'(2)'-O-anthraniloyladenosine 5'-triphosphate. Biochim. Biophys. Acta, 2000, 1478, 289-299. (Pubitemid 30312886)
15. Blaszczyk, J.; Shi, G.; Yan, H.; Ji, X., Catalytic center assembly of HPPK as revealed by the crystal structure of a ternary complex at 1.25 angstrom resolution. Structure 2000, 8, 1049-1058. (Pubitemid 32667468)
16. Garçon, A.; Bermingham, A.; Lian, L.Y.; Derrick, J.P. Kinetic and structural characterization of a product complex of 6-hydroxymethyl-7,8- dihydropterin pyrophosphokinase from Escherichia coli. Biochem. J., 2004, 380, 867-873. (Pubitemid 38850529)
17. Li, G.; Felczak, K.; Shi, G.; Yan, H., Mechanism of the conformational transitions in 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as revealed by NMR spectroscopy. Biochemistry, 2006, 45, 12573-12581. (Pubitemid 44583699)
18. Stammers, D.K.; Achari, A.; Somers, D.O.; Bryant, P.K.; Rosemond, J.; Scott, D.L.; Champness, J.N. 2.0 Å X-ray structure of the ternary complex of 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase from Escherichia coli with ATP and a substrate analogue. FEBS Lett., 1999, 456, 49-53. (Pubitemid 29339039)
19. Blaszczyk, J.; Li, Y.; Shi, G.; Yan, H.; Ji, X. Dynamic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: Crystallographic studies. Biochemistry, 2003, 42, 1573-1580. (Pubitemid 36205964)
20. Blaszczyk, J.; Shi, G.; Li, Y.; Yan, H.; Ji, X. Reaction trajectory of pyrophosphoryl transfer catalyzed by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Structure, 2004, 12, 467-475. (Pubitemid 38353067)
21. Xiao, B.; Shi, G.; Gao, J.; Blaszczyk, J.; Liu, Q.; Ji, X.; Yan, H. Unusual conformational changes in 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as revealed by X-ray crystallography and NMR. J. Biol. Chem., 2001, 276, 40274-40281.
22. Shi, G.; Gao, J.; Yan, H. 1H, 13C and 15N resonance assignments of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase and its complex with MgAMPPCP. J. Biomol. NMR, 1999, 14, 189-190. (Pubitemid 29322976)
23. Lescop, E.; Lu, Z.; Liu, Q.; Xu, H.; Li, G.; Xia, B.; Yan, H.; Jin, C. Dynamics of the Conformational Transitions in the Assembling of the Michaelis Complex of a Bisubstrate Enzyme: A N-15 Relaxation Study of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase. Biochemistry, 2009, 48, 302-312.
24. Keskin, O.; Ji, X.; Blaszcyk, J.; Covell, D.G. Molecular motions and conformational changes of HPPK. Proteins, 2002, 49, 191-205.
25. Yang, R.; Lee, M.C.; Yan, H.; Duan, Y. Loop conformation and dynamics of the Escherichia coli HPPK apo-enzyme and its binary complex with MgATP. Biophys. J., 2005, 89, 95-106. (Pubitemid 41098267)
26. Mildvan, A.S.; Weber, D.J.; Abeygunawrdana, C. Solution structure and mechanism of the MutT pyrophosphohydrolase. Ad. Enzymol. Rel. Areas Mol. Biol., 1999, 73, 183-207.
27. Li, Y.; Wu, Y.; Blaszczyk, J.; Ji, X.; Yan, H. Catalytic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8- dihydropterin pyrophosphokinase: Site-directed mutagenesis and biochemical studies. Biochemistry, 2003, 42, 1581-1588. (Pubitemid 36205965)
28. Blaszczyk, J.; Li, Y.; Wu, Y.; Shi, G.; Ji, X.; Yan, H. Essential roles of a dynamic loop in the catalysis of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Biochemistry, 2004, 43, 1469-1477. (Pubitemid 38200552)