The crystal structure of an algal prolyl 4-hydroxylase complexed with a proline-rich peptide reveals a novel buried tripeptide binding motif

Journal of Biological Chemistry

Volumn 284, Issue 37, 2009, Pages 25290-25301

  Koski, M Kristian ^a   Hieta, Reija ^a   Hirsilä, Maija ^a   Rönkä, Anna ^a   Myllyharju, Johanna ^a   Wierenga, Rik K ^a  

^a UNIVERSITY OF OULU   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

2-OXOGLUTARATE; AROMATIC RESIDUES; BINDING MOTIF; CATALYTIC CYCLES; CATALYTIC DOMAINS; CELL-WALL COMPONENTS; CHLAMYDOMONAS REINHARDTII; CONFORMATIONAL CHANGE; CONFORMATIONAL SWITCHES; HYDROXYLASES; HYPOXIA-INDUCIBLE FACTORS; KEY ENZYMES; KEY FEATURE; L-PROLINE; MODE OF BINDING; MONOMERIC ENZYMES; OXYGEN-SENSING; PEPTIDE BINDING; PEPTIDE SUBSTRATES; PROLINE RESIDUES; PROLYL-4-HYDROXYLASE; SEQUENCE SIMILARITY; SIDE CHAINS; SPECIFIC BINDING; STACKING INTERACTION; TERNARY COMPLEX; TRIPEPTIDE; TYPE II;

AMINES; CATALYSTS; CELL MEMBRANES; COLLAGEN; ENZYMES; HYDROXYLATION; OXYGEN; PEPTIDES; PLANTS (BOTANY); SUBSTRATES; ZINC;

CRYSTAL STRUCTURE;

PROCOLLAGEN PROLINE 2 OXOGLUTARATE 4 DIOXYGENASE; SERYLPROLYLSERINE; TRIPEPTIDE DERIVATIVE; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; CATALYSIS; CHLAMYDOMONAS REINHARDTII; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; CRYSTALLIZATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME CONFORMATION; ENZYME KINETICS; ENZYME SPECIFICITY; ENZYME SUBSTRATE; HYDROGEN BOND; HYDROXYLATION; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN MOTIF; STRUCTURE ANALYSIS;

ALGAE; AMINO ACID MOTIFS; AMINO ACID SEQUENCE; CATALYTIC DOMAIN; COLLAGEN; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; MUTATION; PEPTIDES; PROCOLLAGEN-PROLINE DIOXYGENASE; PROLINE; PROTEIN BINDING; SEQUENCE HOMOLOGY, AMINO ACID;

ALGAE; CHLAMYDOMONAS REINHARDTII; VERTEBRATA;

EID: 69949136771     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M109.014050     Document Type: Article

References (48)

1. Kivirikko, K. I., and Pihlajaniemi, T. (1998) Adv. Enzymol. Relat. Areas Mol. Biol. 72, 325-398
2. Myllyharju, J. (2003) Matrix Biol. 22, 15-24
3. Myllyharju, J., and Kivirikko, K. I. (2004) Trends Genet. 20, 33-43
4. Kieliszewski, M. J., and Lamport, D. T. A. (1994) Plant J. 5, 157-172
5. Cassab, G. I. (1998) Annu. Rev. Plant Physiol. Plant Mol. Biol. 49, 281-309
6. Bruick, R. K., and McKnight, S. L. A. (2001) Science 294, 1337-1340
7. Epstein, A. C., Gleadle, J. M., McNeill, L. A., Hewitson, K. S., O'Rourke, J., Mole, D. R., Mukherji, M., Metzen, E., Wilson, M. I., Dhanda, A., Tian, Y. M., Masson, N., Hamilton, D. L., Jaakkola, P., Barstead, R., Hodgkin, J., Maxwell, P. H., Pugh, C. W., Schofield, C. J., and Ratcliffe, P. J. (2001) Cell 107, 43-54
8. Chowdhury, R., Hardy, A., and Schofield, C. J. (2008) Chem. Soc. Rev. 37, 1308-1319
9. Myllyharju, J. (2008) Ann. Med. 40, 402-417
10. McDonough, M. A., Li, V., Flashman, E., Chowdhury, R., Mohr, C., Liénard, B. M., Zondlo, J., Oldham, N. J., Clifton, I. J., Lewis, J., McNeill, L. A., Kurzeja, R. J., Hewitson, K. S., Yang, E., Jordan, S., Syed, R. S., and Schofield, C. J. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 9814-9819
11. Keskiaho, K., Hieta, R., Sormunen, R., and Myllyharju, J. (2007) Plant Cell 19, 256-269
12. Koski, M. K., Hieta, R., Böllner, C., Kivirikko, K. I., Myllyharju, J., and Wierenga, R. K. (2007) J. Biol. Chem. 282, 37112-37123
13. Jaakkola, P., Mole, D. R., Tian, Y. M., Wilson, M. I., Gielbert, J., Gaskell, S., J., Kriegsheim, Av., Hebestreit, H. F., Mukherji, M., Schofield, C. J., Maxwell, P. H., Pugh, C. W., and Ratcliffe, P. J. (2001) Science 292, 468-472
14. Ivan, M., Kondo, K., Yang, H., Kim, W., Valiando, J., Ohh, M., Salic, A., Asara, J. M., Lane, W. S., and Kaelin, W. G., Jr. (2001) Science 292, 464-468
15. Adair, W. S., and Snell, W. J. (1990) in Organization and Assembly of Plant and Animal Extracellular Matrix (Adair, W. S., and Mecham, R. P., eds) pp. 15-84, Academic Press, San Diego, CA
16. Ferris, P. J., Woessner, J. P., Waffenschmidt, S., Kilz, S., Drees, J., and Goodenough, U. W. (2001) Biochemistry 40, 2978-2987
17. Hieta, R., and Myllyharju, J. (2002) J. Biol. Chem. 277, 23965-23971
18. Clifton, I. J., McDonough, M. A., Ehrismann, D., Kershaw, N. J., Granatino, N., and Schofield, C. J. (2006) J. Inorg. Biochem. 100, 644-669
19. Ozer, A., and Bruick, R. K. (2007) Nat. Chem. Biol. 3, 144-153
20. Newman, J., Egan, D., Walter, T. S., Meged, R., Berry, I., Ben Jelloul, M., Sussman, J. L., Stuart, D. I., and Perrakis, A. (2005) Acta Crystallogr. D Biol. Crystallogr. 61, 1426-1431
21. Bourenkov, G. P., and Popov, A. N. (2006) Acta Crystallogr. D Biol. Crystallogr. 62, 58-64
22. Leslie, A. G. W. (1992) Joint CCP4 ESF-EACBM Newsl. Protein Crystallogr. 26, 22-33
23. Kabsch, W. (1993) J. Appl. Crystallogr. 26, 795-800
24. McCoy, A. J., Grosse-Kunstleve, R. W., Storoni, L. C., and Read, R. J. (2005) Acta Crystallogr. D Biol. Crystallogr. 61, 458-464
25. Emsley, P., and Cowtan, K. (2004) Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132
26. Winn, M. D., Isupov, M. N., and Murshudov, G. N. (2001) Acta Crystallogr. D Biol. Crystallogr. 57, 122-133
27. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Acta Crystallogr. D Biol. Crystallogr. 53, 240-255
28. CCP4 (1994) Acta Crystallogr. D Biol. Crystallogr. 50, 760-763
29. Evrard, G. X., Langer, G. G., Perrakis, A., and Lamzin, V. S. (2007) Acta Crystallogr. D Biol. Crystallogr. 63, 108-117
30. Howlin, B., Butler, S. A., Moss, D. S., Harris, G. W., and Driessen, H. P. C. (1993) J. Appl. Crystallogr. 26, 622-624
31. Davis, I. W., Leaver-Fay, A., Chen, V. B., Block, J. N., Kapral, G. J., Wang, X., Murray, L. W., Arendall, W. B., 3rd, Snoeyink, J., Richardson, J. S., and Richardson, D. C. (2007) Nucleic Acids Res. 35, W375-W383
32. Ball, L. J., Kühne, R., Schneider-Mergener, J., and Oschkinat, H. (2005) Angew. Chem. Int. Ed. 44, 2852-2869
33. Elkins, J. M., Hewitson, K. S., McNeill, L. A., Seibel, J. F., Schlemminger, I., Pugh, C. W., Ratcliffe, P. J., and Schofield, C. J. (2003) J. Biol. Chem. 278, 1802-1806
34. Flashman, E., Bagg, E. A., Chowdhury, R., Mecinovic, J., Loenarz, C., McDonough, M. A., Hewitson, K. S., and Schofield, C. J. (2008) J. Biol. Chem. 283, 3808-3815
35. Yu, B., Edstrom, W. C., Benach, J., Hamuro, Y., Weber, P. C., Gibney, B. R., and Hunt, J. F. (2006) Nature 439, 879-884
36. McDonough, M. A., Kavanagh, K. L., Butler, D., Searls, T., Oppermann, U., and Schofield, C. J. (2005) J. Biol. Chem. 280, 41101-41110
37. Kaska, D. D., Günzler, V., Kivirikko, K. I., and Myllylä, R. (1987) Biochem. J. 241, 483-490
38. Tiainen, P., Myllyharju, J., and Koivunen, P. (2005) J. Biol. Chem. 280, 1142-1148
39. Annunen, P., Helaakoski, T., Myllyharju, J., Veijola, J., Pihlajaniemi, T., and Kivirikko, K. I. (1997) J. Biol. Chem. 272, 17342-17348
40. Zhang, Z., Ren, J., Harlos, K., McKinnon, C. H., Clifton, I. J., and Schofield, C. J. (2002) FEBS Lett. 517, 7-12
41. Hoffart, L. M., Barr, E. W., Guyer, R. B., Bollinger, J. M., Jr., and Krebs, C. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 14738-14743
42. Bollinger, J. M., Jr., Price, J. C., Hoffart, L. M., Barr, E. W., and Krebs, C. (2005) Eur. J. Inorg. Chem. 2005, 4245-4254
43. O'Brien, J. R., Schuller, D. J., Yang, V. S., Dillard, B. D., and Lanzilotta, W. N. (2003) Biochemistry 42, 5547-5554
44. Gorres, K. L., Edupuganti, R., Krow, G. R., and Raines, R. T. (2008) Biochemistry 47, 9447-9455
45. Loenarz, C., Mecinović, J., Chowdhury, R., McNeil, L. A., Flashman, E., and Schofield, C. J. (2009) Angew. Chem. Int. Ed. Engl. 48, 1784-1787
46. Okuyama, K., Hongo, C., Fukushima, R., Wu, G., Narita, H., Noguchi, K., Tanaka, Y., and Nishino, N. (2004) Biopolymers 76, 367-377
47. Schumacher, M., Mizuno, K., and Bächinger, H. P. (2005) J. Biol. Chem. 280, 20397-20403
48. Hon, W. C., Wilson, M. I., Harlos, K., Claridge, T. D., Schofield, C. J., Pugh, C. W., Maxwell, P. H., Ratcliffe, P. J., Stuart, D. I., and Jones, E. Y. (2002) Nature 417, 975-978