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Licensed Unlicensed Requires Authentication Published by De Gruyter June 1, 2005

X-ray structure of fumarylacetoacetate hydrolase family member Homo sapiens FLJ36880

  • Babu A. Manjasetty , Frank H. Niesen , Heinrich Delbrück , Frank Götz , Volker Sievert , Konrad Büssow , Joachim Behlke and Udo Heinemann
From the journal Biological Chemistry

Abstract

The human protein FLJ36880 belongs to the fumarylacetoacetate hydrolase family. The X-ray structure of FLJ36880 has been determined to 2.2 Å resolution employing the semi-automated high-throughput structural genomics approach of the Protein Structure Factory. FLJ36880 adopts a mixed β-sandwich roll fold and forms homodimers in crystals as well as in solution. One Mg2+ ion is bound to each subunit of the dimeric protein by coordination to three carboxylate oxygens and three water molecules. These metal binding sites are accessible from the same surface of the dimer, partly due to the disorder of the undecapeptide stretch D29 to L39. The overall structure and metal binding site of FLJ36880 bear clear similarities to the C-terminal domain of the bifunctional enzyme HpcE from Escherichia coli C, fumarylacetoacetate hydrolase from Mus musculus and to YcgM (Apc5008) from E. coli 1262. These similarities provide a framework for suggesting biochemical functions and evolutionary relationships of FLJ36880. It appears highly probable that the metal binding sites are involved in an enzymatic activity related to the catabolism of aromatic amino acids. Two point mutations in the active-site of FAH, responsible for the metabolic disease hereditary tyrosinemia type I (HTI) in humans, affect residues that are structurally conserved in FLJ36880 and located in the putative catalytic site.

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References

Aponte, J. L., Sega, G. A., Hauser, L. J., Dhar, M. S., Withrow, C. M., Carpenter, D. A., Rinchik, E. M., Culiat, C. T., and Johnson, D. K. (2001). Point mutations in the murine fumarylacetoacetate hydrolase gene: animal models for the human genetic disorder hereditary tyrosinemia type 1. Proc. Natl. Acad. Sci. USA98, 641–645.10.1073/pnas.98.2.641Search in Google Scholar

Bateman, R. L., Bhanumoorthy, P., Witte, J. F., McClard, R. W., Grompe, M., and Timm, D. E. (2001). Mechanistic inferences from the crystal structure of fumarylacetoacetate hydrolase with a bound phosphorus-based inhibitor. J. Biol. Chem.276, 15284–15291.10.1074/jbc.M007621200Search in Google Scholar

Behlke, J., Ristau, O., and Schönfeld, H. J. (1997). Nucleotide-dependent complex formation between the Escherichia coli chaperonins GroEL and GroES studied under equilibrium conditions. Biochemistry36, 5149–5156.10.1021/bi962755hSearch in Google Scholar

Berger, R., Smit, G. P., Stoker-de Vries, S. A., Duran, M., Ketting, D., and Wadman, S. K. (1981). Deficiency of fumarylacetoacetase in a patient with hereditary tyrosinemia. Clin. Chim. Acta114, 37–44.10.1016/0009-8981(81)90225-4Search in Google Scholar

Bergeron, A., D’Astous, M., Timm, D.E., and Tanguay, R.M. (2001). Structural and functional analysis of missense mutations in fumarylacetoacetate hydrolase, the gene deficient in herediatary tyrosinemia type 1. J. Biol. Chem.276, 15225–15231.10.1074/jbc.M009341200Search in Google Scholar

Collaborative Computational Project Number 4 (1994). The CCP4 suite: programs for protein crystallography. Acta Crystallogr.D50, 760–763.10.1107/S0907444994003112Search in Google Scholar

DeLano, W. L. (2003). The PyMOL Molecular Graphics System (San Carlos, CA, USA: DeLano Scientific); http://www.pymol.org.Search in Google Scholar

Garrido-Peritierra, A. and Cooper, R. A. (1981). Identification and purification of distinct isomerase and decarboxylase enzymes involved in the 4-hydroxyphenylacetate catabolic pathway of Escherichia coli. Eur. J. Biochem.117, 581–584.10.1111/j.1432-1033.1981.tb06377.xSearch in Google Scholar

Gibrat, J. F., Madej, T., and Bryant, S. H. (1996). Surprising similarities in structure comparison. Curr. Opin. Struct. Biol.6, 377–385.10.1016/S0959-440X(96)80058-3Search in Google Scholar

Harayama, S., Rekik, M., Ngai, K. L., and Ornston, L. N. (1989). Physically associated enzymes produce and metabolize 2-hydroxy-2,4-dienoate, a chemically unstable intermediate formed in catechol metabolism via meta cleavage in Pseudomonas putida. J. Bacteriol.171, 6251–6258.10.1128/jb.171.11.6251-6258.1989Search in Google Scholar PubMed PubMed Central

Heinemann, U., Büssow, K., Mueller, U., and Umbach, P. (2003). Facilities and methods for the high-throughput crystal structural analysis of human proteins. Acc. Chem. Res.36, 157–163.10.1021/ar010129tSearch in Google Scholar PubMed

Jones, S. and Thornton, J. M. (1995). Protein-protein interactions: a review of protein dimer structures. Prog. Biophys. Mol. Biol., 63, 31–65.10.1016/0079-6107(94)00008-WSearch in Google Scholar

Jones, T. A., Zhou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr.D49, 18–23.10.1107/S0108767390010224Search in Google Scholar

Kraulis, P. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr.24, 946–950.10.1107/S0021889891004399Search in Google Scholar

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, 283–291.10.1107/S0021889892009944Search in Google Scholar

Matthews, B. W. (1968). Solvent content of protein crystals. J. Mol. Biol.33, 491–497.10.1016/0022-2836(68)90205-2Search in Google Scholar

McIninch, J. K., McIninch, J. D., and May, S. W. (2003). Catalysis, stereochemistry, and inhibition of ureidoglycolate lyase. J. Biol. Chem.278, 50091–50100.10.1074/jbc.M303828200Search in Google Scholar

Mueller, U., Nyarsik, L., Horn, M., Rauth, H., Przewieslik, T., Saenger, W., Lehrach, H. and Eickhoff, H. (2001). Development of a technology for automation and miniaturization of protein crystallization. J. Biotechnol.85, 7–14.10.1016/S0168-1656(00)00349-7Search in Google Scholar

Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997). Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr.D53, 240–255.10.1107/S0907444996012255Search in Google Scholar

Otwinowski, Z. and Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol.276, 307–326.10.1016/S0076-6879(97)76066-XSearch in Google Scholar

Overturf, K., Al-Dhalimy, M., Tanguay, R., Brantly, M., Ou, C. N., Finegold, M., and Grompe, M. (1996). Hepatocytes corrected by gene therapy are selected in vivo in a murine model of hereditary tyrosinaemia type I. Nat. Genet.12, 266–273.10.1038/ng0396-266Search in Google Scholar PubMed

Perrakis, A., Harkiolaki, M., Wilson, K. S., and Lamzin, V. S. (2001). ARP/wARP and molecular replacement. Acta Crystallogr.D57, 1445–1450.10.1107/S0907444901014007Search in Google Scholar

Prieto, M. A., Diaz, E., and Garcia, J. L. (1996). Molecular characterization of the 4-hydroxyphenylacetate catabolic pathway of Escherichia coli W: engineering a mobile aromatic degradative cluster. J. Bacteriol.178, 111–120.10.1128/jb.178.1.111-120.1996Search in Google Scholar

Schwede, T., Kopp, J., Guex, N., and Peitsch, M. C. (2003). SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res.31, 3381–3385.10.1093/nar/gkg520Search in Google Scholar

St-Louis, M. and Tanguay, R.M. (1997). Mutations in the fumarylacetoacetate hydrolase gene causing hereditary tyrosinemia type I: overview. Hum. Mutat.9, 291–299.10.1002/(SICI)1098-1004(1997)9:4<291::AID-HUMU1>3.0.CO;2-9Search in Google Scholar

Tame, J. R., Namba, K., Dodson, E. J., and Roper, D. I. (2002). The crystal structure of HpcE, a bifunctional decarboxylase/isomerase with a multifunctional fold. Biochemistry41, 2982–2989.10.1021/bi015717tSearch in Google Scholar

Timm, D. E., Mueller, H. A., Bhanumoorthy, P., Harp, J. M., and Bunick, G. J. (1999). Crystal structure and mechanism of a carbon-carbon bond hydrolase. Structure Fold. Des.7, 1023–1033.10.1016/S0969-2126(99)80170-1Search in Google Scholar

Vagin, A. and Teplyakov, A. (2000). An approach to multi-copy search in molecular replacement. Acta Crystallogr.D56, 1622–1624.10.1107/S0907444900013780Search in Google Scholar

Vaguine, A. A., Richelle, J., and Wodak, S. J. (1999). SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr.D55, 191–205.10.1107/S0907444998006684Search in Google Scholar

Wiemann, S., Weil, B., Wellenreuther, R., Gassenhuber, J., Glassl, S., Ansorge, W., Böcher, M., Blöcker, H., Bauersachs, S., Blum, H. et al. (2001). Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. Genome Res.11, 422–435.10.1101/gr.154701Search in Google Scholar

Published Online: 2005-06-01
Published in Print: 2004-10-01

© Walter de Gruyter

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