X-ray structure of a putative reaction intermediate of 5-aminolaevulinic acid dehydratase

Biochemical Journal

Volumn 373, Issue 3, 2003, Pages 733-738

  Erskine, Peter T ^a   Coates, Leighton ^a   Butler, Danica ^a   Youell, James H ^a   Brindley, Amanda A ^b   Wood, Steve P ^a   Warren, Martin J ^b   Shoolingin Jordan, Peter M ^a   Cooper, Jonathan B ^a  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^b School of Biological and Chemical Sciences   (United Kingdom)

Author keywords

5 aminolaevulinic acid dehydratase; Catalytic mechanism; Reaction intermediate; Trapped intermediate; X ray structure

Indexed keywords

CHEMICAL BONDS; ENZYMES; X RAY ANALYSIS; YEAST;

BOND LINKING;

BIOCHEMISTRY;

PORPHOBILINOGEN SYNTHASE;

ARTICLE; CATALYSIS; CHEMICAL STRUCTURE; COVALENT BOND; ENZYME ACTIVE SITE; ENZYME SUBSTRATE; PRIORITY JOURNAL; X RAY ANALYSIS;

CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; PORPHOBILINOGEN SYNTHASE; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; SACCHAROMYCES CEREVISIAE;

EID: 0042569086     PISSN: 02646021     EISSN: None     Source Type: Journal    
DOI: 10.1042/BJ20030513     Document Type: Article

References (32)

1. Jordan, P. M. (1991) Biosynthesis of tetrapyrroles. New Compr. Biochem. 19, 1-65
2. Jordan, P. M. (1994) Highlights in haem biosynthesis. Curr. Opin. Struc. Mol. Biol. 4, 902-911
3. Warren, M. J. and Scott, A. I. (1990) Tetrapyrrole assembly and modification into the ligands of biologically functional cofactors. Trends Biochem. Sci. 15, 486-491
4. Jaffe, E. K. (1995) Porphobilinogen synthase, the first source of heme's asymmetry. J. Bioenerg. Biomembr. 27, 169-179
5. Jaffe, E. K. (2003) Unusual phylogenetic variation in the metal ion binding sites of porphobilinogen synthase. Chem. Biol. 10, 25-34
6. Doss, M., Von-Tieperman, R., Schneider, J. and Schmid, H. (1979) New types of hepatic porphyria with porphobilinogen synthase defect and intermittent acute clinical manifestation. Klin. Wochenschr. 57, 1123-1127
7. 2+. Eur. J. Biochem. 234, 178-183
8. Warren, M. J., Cooper, J. B., Wood, S. P. and Shoolingin-Jordan, P. M. (1998) Lead poisoning, haem synthesis and 5-aminolevulinic acid dehydratase. Trends Biochem. Sci. 23, 217-221
9. Erskine, P. T., Senior, N., Awan, S., Lambert, R., Lewis, G., Tickle, I. J., Sarwar, M., Spencer, P., Thomas, P., Warren, M. J., Shoolingin-Jordan, P. M. et al. (1997) X-ray structure of 5-aminolevulinate dehydratase, a hybrid aldolase. Nat. Struct. Biol. 4, 1025-1031
10. Erskine, P. T., Norton, E., Cooper, J. B., Lambert, R., Coker, A., Lewis, G., Spencer, P., Sarwar, M., Wood, S. P., Warren, M. J. and Shoolingin-Jordan, M. J. (1999) The X-ray structure of 5-aminolevulinic acid dehydratase from Escherichia coli complexed with the inhibitor levulinic acid at 2.0 Å resolution. Biochemistry 38, 4266-4276
11. 2+-dependent porphobilinogen synthase. J. Mol. Biol. 289, 591-602
12. Mills-Davies, N. L. (2001) Structure of human erythrocyte 5-aminolaevulinic acid dehydratase, the second enzyme in the biosynthesis of haem. Ph.D. Thesis, University of Southampton
13. Jordan, P. M. and Gibbs, P. N. B. (1985) Mechanism of action of 5-aminolevulinate dehydratase from human erythrocytes. Biochem. J. 227, 1015-1020
14. Gibbs, P. N. B. and Jordan, P. M. (1986) Identification of a lysine at the active site of human 5-aminolevulinate dehydratase. Biochem. J. 236, 447-451
15. Boese, Q. F., Spano, A. J., Li, J. and Timko, M. P. (1991) 5-Aminolevulinic acid dehydratase in pea. Identification of an unusual metal-binding domain in the plant enzyme. J. Biol. Chem. 266, 17060-17066
16. Erskine, P. T., Newbold, R., Brindley, A. A., Wood, S. P., Shoolingin-Jordan, P. M., Warren, M. J. and Cooper, J. B. (2001) The X-ray structure of yeast 5-aminolaevulinic acid dehydratase complexed with substrate and three inhibitors. J. Mol. Biol. 312, 133-141
17. Erskine, P. T., Coates, L., Newbold, R., Brindley, A. A., Stauffer, F., Wood, S. P., Warren, M. J., Cooper, J. B., Shoolingin-Jordan, P. M. and Neier, R. (2001) The X-ray structure of yeast 5-aminolaevulinic acid dehydratase complexed with two diacid inhibitors. FEBS Lett. 503, 196-200
18. Kervinen, J., Jaffe, E. K., Stauffer, F., Neier, R., Wlodawer, A., Zdanov, A. (2001) Mechanistic basis for suicide inactivation of porphobilinogen synthase by 4,7-dioxosebacic acid, an inhibitor that shows dramatic species selectivity. Biochemistry 40, 8227-8236
19. Frère, F., Schubert, W.-D., Stauffer, F., Frankenberg, N., Neier, R., Jahn, D. and Heinz, D. W. (2002) Structure of porphobilinogen synthase from Pseudomonas aeruginosa in complex with 5-fluorolevulinic acid suggests a double Schiff base mechanism. J. Mol. Biol. 320, 237-247
20. Neier, R. (1996) Chemical synthesis of porphobilinogen and studies of its biosynthesis. Adv. Nitrogen Heterocycl. 2, 35-146
21. Erskine, P. T., Senior, N., Maignan, S., Cooper, J., Lambert, R., Lewis, G., Spencer, P., Awan, S., Warren, M., Tickle, I. J. et al. (1997) Crystallisation of 5-aminolevulinic acid dehydratase from Escherichia coli and Saccharomyces cerevisiae and preliminary X-ray characterisation of the crystals. Protein Sci. 6, 1774-1776
22. Leslie, A. G. W. (1992) Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4+ESF-EAMCB Newsletter on Protein Crystallography, No. 26, Daresbury Laboratories, Warrington, U.K.
23. CCP4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50, 760-763
24. Sheldrick, G. M. and Schneider, T. R. (1997) SHELXL: high-resolution refinement. Methods Enzymol. 277, 319-343
25. Haneef, I., Moss, D. S., Stanford, M. J. and Borkakoti, N. (1985) Restrained structure-factor least-squares refinement of protein structures using a vector-processing computer. Acta Crystallogr. A41, 426-433
26. Laskowski, R. A., MacArthur, M. W., Moss, D. S. and Thornton, J. M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291
27. Erskine, P. T., Newbold, R., Roper, J., Coker, A., Warren, M. J., Shoolingin-Jordan, P. M., Wood, S. P. and Cooper, J. B. (1999) The Schiff base complex of yeast 5-aminolaevulinic acid dehydratase with laevulinic acid. Protein Sci. 8, 1250-1256
28. Jaffe, E. K., Markham, G. D. and Rajogopalan, J. S. (1990) N-15 and C-13 NMR-studies of ligands bound to the 280,000-Dalton protein porphobilinogen synthase elucidate the structures of enzyme-bound product and a Schiff-base intermediate. Biochemistry 29, 8345-8350
29. Butler, D. (2003) Characterisation and crystallisation of human 5-aminolaevulinic acid dehydratase and porphobilinogen deaminase.
30. Mauzerall, D. and Granick, S. (1956) The occurrence and determination of δ-aminolevulinic acid and porphobilinogen in urine. J. Biol. Chem. 219, 435-446
31. Chaudhry, A. G. and Jordan, P. M. (1976) Stereochemical studies on the formation of porphobilinogen. Biochem. Soc. Trans. 4, 760-761
32. Read, R. J. (1986) Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A42, 140-149