Structural basis for tetrapyrrole coordination by uroporphyrinogen decarboxylase

EMBO Journal

Volumn 22, Issue 23, 2003, Pages 6225-6233

  Phillips, John D ^a   Whitby, Frank G ^a   Kushner, James P ^a   Hill, Christopher P ^a  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

Crystallography; Enzyme mechanism; Enzyme product complex; Protein structure; Uroporphyrinogen decarboxylase

Indexed keywords

ACETIC ACID DERIVATIVE; ASPARTIC ACID; CARBOXYLIC ACID; COPROPORPHYRINOGEN; HEME DERIVATIVE; MUTANT PROTEIN; PORPHYRINOGEN; PYRROLE DERIVATIVE; TETRAPYRROLE; UNCLASSIFIED DRUG; UROPORPHYRINOGEN; UROPORPHYRINOGEN DECARBOXYLASE;

ARTICLE; CATALYSIS; CRYSTALLIZATION; DECARBOXYLATION; ENZYME STRUCTURE; ENZYME SUBSTRATE; GEOMETRY; HEME SYNTHESIS; HUMAN; HYDROGEN BOND; MUTATION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FUNCTION; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; ANIMALS; ASPARTIC ACID; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; HYDROGEN BONDING; IMAGE PROCESSING, COMPUTER-ASSISTED; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS; TETRAPYRROLES; UROPORPHYRINOGEN DECARBOXYLASE;

EID: 0347504852     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/cdg606     Document Type: Article

References (29)

1. Akhtar, M. (1994) The modification of acetate and propionate side chains during the biosynthesis of haem and chlorophylls: mechanistic and stereochemical studies. In Ciba Foundation Symposium (ed.) The Biosynthesis of the Tetrapyrrole Pigments. John Wiley and Sons Ltd, Chichester, NY, USA. Vol. 180, pp. 131-155.
2. Appleby, T.C., Kinsland, C., Begley, T.P. and Ealick, S.E. (2000) The crystal structure and mechanism of orotidine 5′-monophosphate decarboxylase. Proc. Natl Acad. Sci. USA, 97, 2005-2010.
3. Bernard, G.F. and Akhtar, M. (1979) Stereochemical and mechanistic studies on the decarboxylation of uroporphyrinogen III in haem biosynthesis. J. C. S. Perkin 1, 10, 2354-2360.
4. Boeker, E.A. and Snell, E.E. (1972) Amino acid decarboxylases. In Boyer, P.D. (ed.) The Enzymes. Academic Press, New York, Vol. 6, pp. 217-254.
5. CCP4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D, 50, 760-763.
6. Feng, W.Y., Austin, T.J., Chew, F., Gronert, S. and Wu, W. (2000) The mechanism of orotidine 5′-monophosphate decarboxylase: catalysis by destabilization of the substrate. Biochemistry, 39, 1778-1783.
7. Gallagher, T., Snell, E.E. and Hackert, M.L. (1989) Pyruvoyl-dependent histidine decarboxylase. Active site structure and mechanistic analysis. J. Biol. Chem., 264, 12737-12743.
8. Grishin, N.V., Osterman, A.L., Brooks, H.B., Phillips, M.A. and Goldsmith, E.J. (1999) X-ray structure of ornithine decarboxylase from Trypanosoma brucei: the native structure and the structure in complex with α-difluoromethylornithine. Biochemistry, 38, 15174-15184.
9. Guex, N. and Peitsch, M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.
10. Held, J.L., Sassa, S., Kappas, A. and Harber, L.C. (1989) Erythrocyte uroporphyrinogen decarboxylase activity in porphyria cutanea tarda: a study of 40 consecutive patients. J. Invest. Dermatol., 93, 332-334.
11. Jackson, A.H., Sancovich, H.A., Ferrmola, A.M., Evans, N., Games, D.E., Matlin, S.A., Elder, G.H. and Smith, S.G. (1976) Macrocyclic intermediates in the biosynthesis of porphyrins. Phil. Trans. R. Soc. Lond. Series B, 273, 191-206.
12. Jones, T.A., Zou, J.-Y., Cowan, S.W. and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and location of errors in these models. Acta Crystallogr. A, 47, 110-119.
13. Kappas, A., Sassa, S., Galbraith, R.A. and Nordmann, Y. (1995) The porphyrias. In Scriver, C.R., Beaudet, A.L., Sly, W.S. and Valle, D. (eds) The Metabolic and Molecular Bases of Inherited Disease. McGraw-Hill, New York, pp. 2103-2160.
14. Kraulis, P.J. (1991) Molscript: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr., 24, 946-950.
15. Kushner, J.P., Barbuto, A.J. and Lee, G.R. (1976) An inherited enzymatic defect in porphyria cutanea tarda: decreased uroporphyrinogen decarboxylase activity. J. Clin. Invest., 58, 1089-1097.
16. Martins, B.M., Grimm, B., Mock, H.P., Huber, R. and Messerschmidt, A. (2001) Crystal structure and substrate binding modeling of the uroporphyrinogen-III decarboxylase from nicotiana tabacum: implications for the catalytic mechanism. J. Biol. Chem., 276, 44108-44116.
17. Mathews, M.A.A., Schubert, H.L., Whitby, F.G., Alexander, K.J., Schadick, K., Bergonia, H.A., Phillips, J.D. and Hill, C.P. (2001) Crystal structure of human uroporphyrinogen III synthase. EMBO J., 20, 5832-5839.
18. Merritt, E.A. and Bacon, D.J. (1997) Raster3D: photorealistic molecular graphics. In Carter, C.W.J. and Sweet, R.M. (eds) Methods in Enzymology. Academic Press, Vol. 277, pp. 505-524.
19. Murshudov, G.N., Vagin, A.A. and Dodson, E.J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D, 53, 240-255.
20. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. In Carter, C.W.J. and Sweet, R.M. (eds) Methods in Enzymology. Academic Press, Vol. 276, pp. 307-326.
21. Phillips, J.D. and Kushner, J.P. (1999) Measurement of uroporphyrinogen decarboxylase activity. In Current Protocols in Toxicology. John Wiley and Sons, Inc., New York, pp. 8.4.1-8.4.13.
22. Phillips, J.D., Whitby, F.G., Kushner, J.P. and Hill, C.P. (1997) Characterization and crystallization of human uroporphyrinogen decarboxylase. Protein Sci., 6, 1343-1346.
23. Phillips, J.D., Jackson, L.K., Bunting, M., Franklin, M.R., Thomas, K.R., Levy, J.E., Andrews, N.C. and Kushner, J.P. (2001) A mouse model of familial porphyria cutanea tarda. Proc. Natl Acad. Sci. USA, 98, 259-264.
24. Straka, J.G. and Kushner, J.P. (1983) Purification and characterization of bovine hepatic uroporphyrinogen decarboxylase. Biochemistry, 22, 4664-4672.
25. Warshel, A., Florian, J., Strajbl, M. and Villa, J. (2001) Circe effect versus enzyme preorganization: what can be learned from the structure of the most proficient enzyme? Chembiochem, 2, 109-111.
26. Whitby, F.G., Phillips, J.D., Kushner, J.P. and Hill, C.P. (1998) Crystal structure of human uroporphyrinogen decarboxylase. EMBO J., 17, 2463-2471.
27. Woodcock, S.C. and Jordan, P.M. (1994) Evidence for participation of aspartate-84 as a catalytic group at the active site of porphobilinogen deaminase obtained by site-directed mutagenesis of the hemC gene from Escherichia coli. Biochemistry, 33, 2688-2695.
28. Wu, N., Mo, Y., Gao, J. and Pai, E.F. (2000) Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase. Proc. Natl Acad. Sci. USA, 97, 2017-2022.
29. Wyckoff, E.E. and Kushner, J.P. (1994) Heme biosynthesis, the porphyrias and the liver. In Arias, I.M., Boyer, J.L., Fausto, N., Jakoby, W.B., Schachter, D.A. and Shafritz, D.A. (eds) The Liver: Biology and Pathobiology. Raven Press Ltd, New York, pp. 505-527.