3-羟基邻氨基苯甲酸3，4-双氧化酶（3HAO）的结构和功能研究
|
摘要
3-羟基邻氨基苯甲酸3，4-双氧化酶(3HAO)是色氨酸犬尿氨酸代谢途径的一个非血红素Fe~(2+)离子外二醇双氧化酶。其催化3-羟基邻氨基苯甲酸转化为喹啉酸。喹啉酸是NAD~+生物合成的前体，同时也是N-甲基-D-天冬氨酸(NMDA)受体的激动剂从而引发神经毒。酵母3HAO的2.4(?)分辨率的晶体结构证实其是功能多样化的Cupin超家族的一员。酵母3HAO晶体结构是至今解析的第一个真核的3HAO的结构，形成同二聚体，每个分子有两个Ni~(2+)离子的结合位点，其中一个Ni~(2+)离子占据了活性中心非血红素Fe~(2+)离子位置，此活性中心位于一个保守的β桶折叠为特征的结构域中。分析结构可看出参与催化的一系列残基有别于其它的外二醇双氧化酶，Asp120、Asn51、Glu111、和Arg114与两个配位活性中心Fe~(2+)离子的残基(His49和Glu55)形成一氢键网络，此氢键网络在3HAO的催化过程中起重要作用。残基Arg101、Gln59和结合底物的疏水口袋决定了底物的特异性。与3HAO from Ralstonia metallidurans的结构比较，活性位点的相似说明原核和真核的3HAO催化机理是相同的。基于序列比较，在Cupin超家族中，我们推测3HAO是从低等生物的单cupin二体向后尘动物的双cupin的单体进化。另一金属离子结合位点我们推测仅仅起结构稳定的作用。基于底物与酵母3HAO模拟复合物的结构，我们提出3HAO可能的反应机理。同时我们认为4-Cl-3-羟基-邻氨基苯甲酸的基于机理的3HAO失活机制是由于Cl原子空间效应的缘故阻碍了底物C3与氧的结合。
3-Hydroxyanthranilic acid 3,4-dioxygenase (3HA0) is a non-heme ferrous
extradiol dioxygenase in the kynurenine pathway from tryptophan. It catalyzes
the conversion of 3-hydroxyanthranilate (HAA) to quinolinic acid (QUIN), an
endogenous neurotoxin, via the activation of N-methyl-D-aspartate (NMDA)
receptors and the precursor of NAD+ biosynthesis. The crystal structure of
3HA0 from S. cerevisiae at 2.4 (?) resolution shows it to be a member of the
functionally diverse cupin superfamily. The structure represents the first
eukaryotic 3HA0 to be resolved. The enzyme forms homodimers, with two
nickel binding sites per molecule. One of the bound nickel atoms occupies the
proposed ferrous-coordinated active site, which is located in a conserved
double-strand β-helix domain. Examination of the structure reveals the
participation of a series of residues in catalysis different from other extradiol
dioxygenases. Together with two iron-binding residues (His49 and Glu55),
Asp120, Asn51, Glu111, and Arg114 form a hydrogen-bonding network; this
hydrogen-bond network is key to the catalysis of 3HAO. Residues Arg101,
Gln59, and the substratebinding hydrophobic pocket are crucial for substrate
specificity. Structure comparison with 3HA0 from Ralstonia metallidurans
reveals similarities at the active site and suggests the same catalytic
mechanism in prokaryotic and eukaryotic 3HAO. Based on sequence
comparison, we suggest that bicupin of human 3HA0 is the first example of
evolution from a monocupin dimer to bicupin monomer in the diverse cupin
superfamilies. A structural stabilization role is proposed for the other metal
binding site. Based on the model of the substrate HAA at the active site of
Y3HAO, we propose a mechanism of catalysis for 3HAO. One possibility of
The Mechanism of Inactivation of 3-Hydroxyanthranilate-3,4-dioxygenase by
4-Chloro-3-hydroxyanthranilate is that the chloro substituent perturbs the
substrate binding in such a way that the addition of oxygen of the C3 carbon of
the substrate is blocked.
3-Hydroxyanthranilic acid 3,4-dioxygenase (3HA0) is a non-heme ferrous
extradiol dioxygenase in the kynurenine pathway from tryptophan. It catalyzes
the conversion of 3-hydroxyanthranilate (HAA) to quinolinic acid (QUIN), an
endogenous neurotoxin, via the activation of N-methyl-D-aspartate (NMDA)
receptors and the precursor of NAD+ biosynthesis. The crystal structure of
3HA0 from S. cerevisiae at 2.4 (?) resolution shows it to be a member of the
functionally diverse cupin superfamily. The structure represents the first
eukaryotic 3HA0 to be resolved. The enzyme forms homodimers, with two
nickel binding sites per molecule. One of the bound nickel atoms occupies the
proposed ferrous-coordinated active site, which is located in a conserved
double-strand β-helix domain. Examination of the structure reveals the
participation of a series of residues in catalysis different from other extradiol
dioxygenases. Together with two iron-binding residues (His49 and Glu55),
Asp120, Asn51, Glu111, and Arg114 form a hydrogen-bonding network; this
hydrogen-bond network is key to the catalysis of 3HAO. Residues Arg101,
Gln59, and the substratebinding hydrophobic pocket are crucial for substrate
specificity. Structure comparison with 3HA0 from Ralstonia metallidurans
reveals similarities at the active site and suggests the same catalytic
mechanism in prokaryotic and eukaryotic 3HAO. Based on sequence
comparison, we suggest that bicupin of human 3HA0 is the first example of
evolution from a monocupin dimer to bicupin monomer in the diverse cupin
superfamilies. A structural stabilization role is proposed for the other metal
binding site. Based on the model of the substrate HAA at the active site of
Y3HAO, we propose a mechanism of catalysis for 3HAO. One possibility of
The Mechanism of Inactivation of 3-Hydroxyanthranilate-3,4-dioxygenase by
4-Chloro-3-hydroxyanthranilate is that the chloro substituent perturbs the
substrate binding in such a way that the addition of oxygen of the C3 carbon of
the substrate is blocked.
引文
Adam, V., Royant, A., Nivie're, V., Molina-Heredia, F.P., Bourgeois, D. 2004. Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion upon X-Ray-Induced Photo-Reduction. Structure 12: 1729-1740.
Anand, R., Dorrestein, P.C., Kinsland, C, Begley, T. P., and Ealick, S.E. 2002. Structure of Oxalate Decarboxylase from Bacillus subtilis at 1.75 A Resolution. Biochemistry 41: 7659-7669.
Bassan, A., Borowski T., and Siegbahn. P.E.M. 2004. Quantum chemical studies of dioxygen activation by mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad. DaltonTrans 2004: 3153-3162.
Brunger, A. T., et al. 1998. Crystallography and N. M. R. system: a new software suite for macromolecular structure determination. Acta Cystallogr. D 54, 905-921.
Bugg, T. D. H., and Lin, G. 2001. Solving the riddle of the intradiol and extradiol catechol dioxygenases: how do enzymes control hydroperoxide rearrangements? Chem. Commun. 941-952.
Bugg, T. D., Sanvoisin, J., Spence, E. L. 1997. Exploring the catalytic mechanism of the extradiol catechol dioxygenases. Biochem. Soc. Trans.25: 81-85.
Calderone, V., Trabucco, M, Menin, V., Negro, A. 2002. Cloning of human 3-hydroxyanthranilic acid dioxygenase in Escherichia coli: characterisation of the purified enzyme and its in vitro inhibition by Zn~(2+) . Biochimica et Biophysica Acta 1596: 283-292.
Cleasby, A., Wonacott, A., Skarzynski, T., Hubbard, R.E., Davies, G.J., Proudfoot, A.E., Bernard, A.R., Payton, M.A., Wells, T.N. 1996. The x-ray crystal structure of phosphomannose isomerase from Candida albicans at 1.7 angstrom resolution. Nat Struct Biol. 3: 470-9.
Colabroy, K. L., Zhai, H., Li, T., Ge, Y., Zhang, Y., Liu, A., Ealick, S.E., McLafferty, F.W., Begley, T.P. 2005. The Mechanism of Inactivation of 3-Hydroxyanthranilate-3,4-dioxygenase by 4-Chloro-3-hydroxyanthranilate, Biochemistry 44: 7623-7631.
Costas, M., Mehn, M.P., Jensen, M.P., Jr. Que, L. 2004. Dioxygen Activation at Mononuclear Nonheme Iron Active Sites: Enzymes, Models, and Intermediates., Jr. Chem.Rev. 104: 936-986.
Cowtan, K. 1999. Error estimation and bias correction in phase-improvement calculations. Acta Crystallogr. D. Biol. Crystallogr. 55: 1555-1567.
Dunwell, J.M., Culham, A., Carter, C.E., Sosa-Aguirre, C.R., and Goodenough, P.W. 2001. Evolution of functional diversity in the cupin superfamily. TRENDS in Biochemical Sciences 26:740-746.
Dunwell, J.M., Purvis, A., Khuri, S. 2004. Cupins: the most functionally diverse protein superfamily? Phytochemistry 65: 7-17.
Fritze, I.M., Linden, L., Freigang, J., Auerbach, G., Huber, R., and Steinbacher, S. 2004. The Crystal Structures of Zea mays and Arabidopsis 4-Hydroxyphenylpyruvate Dioxygenase. Plant Physiology 134: 1388-1400.
Gerlt, J.A., Babbitt, P.C. 2001.DIVERGENT EVOLUTION OF ENZYMATIC FUNCTION: Mechanistically Diverse Superfamilies and Functionally Distinct Suprafamilies. 70: 209-246.
Gopal, B., Madan, L.L. Betz, S.F. and Kossiakoff, A.A. 2005. The Crystal Structure of a Quercetin 2,3-Dioxygenase from Bacillus subtilis Suggests Modulation of Enzyme Activity by a Change in the Metal Ion at the Active Site(s). Biochemistry 44: 193-201.
Gouet, P., Courcelle, E., Stuart, D.I., and Metoz, F. 1999. ESPript: Multiple sequence alignments in PostScript. Bioinformatics 15: 305-308.
Guidetti, P., Luthi-Carter, R.E., Augood, S.J., and Schwarcz, R. 2004. Neostriatal and cortical quinolinate levels are increased in early grade Huntington's disease. Neurobiology of Disease 17: 455-461.
Hasegawa, Y., Muraki, T., Tokuyama,T., Iwaki, H., Tatsuno, M., Lau, P.C.K. 2000. A novel degradative pathway of 2-nitrobenzoate via 3-hydroxyanthranilate in Pseudomonas fuorescens strain K.U-7. FEMS Microbiology Letter 190: 185-190.
Heyes, M.P., Achim, C.L., Wiley, C.A., Major,E.O., Saito, K., and Markey, S.P. 1996.
Human microglia convert L-tryptophan into the neurotoxin quinolinic acid. biochem.J. 320: 595-597.
Heyes, M. P., Saito, K., Jacobowitz, D., Markey, S. P., Takikawa, O., and Vickers, J. H. 1992. Poliovirus induces indoleamine-2,3-dioxygenase and quinolinic acid synthesis in macaque brain. FASEB J. 6: 2977-89.
Koehntop, K.D., Emerson, J.P., and Jr Que, L. 2005. The 2-His-1-carboxylate facial triad: a versatile platform for dioxygen activation by mononuclear non-heme iron(II) enzymes. Journal of Biological Inorganic Chemistry 10: 87-93.
Koontz, W.A., and Shiman, R. 1976. Beef Kidney 3-Hydroxyanthranilic Acid Oxygenase PURIFICATION, CHARACTERIZATION, AND ANALYSIS OF THE ASSAY J. Biol. Chem. 251: 368-377.
Kucharczyka, R., Zagulskia, M, Rytkaa, J., Herbertb, C.J. 1998. The yeast gene YJR025c encodes a 3-hydroxyanthranilic acid dioxygenase and is involved in nicotinic acid biosynthesis. FEBS Letters 424: 127-130.
Kurnasov, O., Goral, V., Colabroy, K., Gerdes, S., Anantha, S., Osterman, A., and Begley, T. P. 2003. NAD biosynthesis: identification of the tryptophan to quinolinate pathway in bacteria.Chem . Biol. 10: 1195-204.
La Fortelle, E. de, Irwin, J.J., and Bricogne, G. 1997. SHARP: A maximum-likelihood heavy-atom parameter refinement and phasing program for the MIR and MAD methods. In Crystallographic computing (eds. P. Bourne and K. Watenpaugh), pp. 250-262. IUCR, Oxford, UK.
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.
Lendenmann, U., Spain, J.C. 1996. 2-Aminophenol 1,6-Dioxygenase: a Novel Aromatic Ring Cleavage Enzyme Purified from Pseudomonas pseudoalcaligenes JS45. Journal of Bacteriolog. 178:6227-6232.
Malherbe, P, Koehler, C, Da Prada, M., Lang, G., Kiefer, V., Schwarcz, R., Lahm, H.-W., and Cesura, A. M. 1994. Molecular cloning and functional expression of human 3-hydroxyanthranilicacid dioxygenase,.J Biol. Chem. 269:13792-7.
Matthews, B.W. 1968. Solvent content of protein crystals. J. Mol. Biol. 33: 491-497.
Mendel, S., Arndt,A., and Bugg, T. D. H. 2004. Acid-Base Catalysis in the Extradiol Catechol Dioxygenase Reaction Mechanism: Site-Directed Mutagenesis of His-115 and His-179 in Escherichia coli 2,3-Dihydroxyphenylpropionate 1,2-Dioxygenase (MhpB). Biochemistry 43: 13390-13396.
Mitchell,R.A.,Kang,H.H.,and Henderson, L.M. 1963. Inactivation during Functioning of 3-Hydroxyanthranilate Oxidase Resulting from Oxidation of Bound Ferrous Iron. J. Biol. Chem. 238: 1151-1155.
Muraki,T., Taki, M.. Hasegawa, Y.. Iwaki, H., Lau, P.C.K. 2003. Prokaryotic Homologs of the Eukaryotic 3-Hydroxyanthranilate 3,4-Dioxygenase and 2-Amino-3-Carboxymuconate-6-Semialdehyde Decarboxylase in the 2-Nitrobenzoate Degradation Pathway of Pseudomonas fluorescens Strain KU-7. Applid And Environmental Microbiology 69:1564-1572.
Murakami,S., Sawami, Y., Takenaka, S., and Aoki,K. 2004 Cloning of a gene encoding 4-amino-3-hydroxybenzoate 2,3-dioxygenase from Bordetella sp. 10d. Biochemical and Biophysical Research Communications 314: 489-494.
Murshudov. G.N., Vagin, A.A., Dodson. E.J. (1997). Refinement of Macromolecular Structures by the Maximum-Likelihood Method. Acta Cryst. D53: 240-255.
Murzin,A.G., Brenner,S.E., Hubbard.T., Chothia,C. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures.J. Mol. Biol. 247:536-540.
Nandi, D., Lightcap, E.S., Koo, Y. K., Lu, X.L., Quancard, J., Silverman, R.B. 2003. Purification and inactivation of 3-hydroxyanthranilic acid 3,4-dioxygenase from beef liver. The International Journal of Biochemistry & Cell Biology 35: 1085-1097.
Nogales, J., Canales, A., Jimenez-Barbero, J., Garcia, J. L., and Diaz, E. 2005.
Molecular Characterization of the Gallate Dioxygenase from Pseudomonas putida KT2440: the Prototype of a New Subgroup of Extradiol Dioxygenases. J. Biol. Chem.280: 35382-90.
Otwinowski, Z. and Minor, W. 1997. Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276A: 307-326.
Pandey, J., Paul. D,, Jain, R.K. 2003. Branching of o-nitrobenzoate degradation pathway in Arthrobacter protophormiae RKJ 100: identification of new intermediates. FEMS Microbiology Letters 229:231-236,
Parli, C.J., Krieter, P., and Schmidt, B. 1980. Metabolism of 6-chlorotryptophan to 4-chloro-3-hydroxyanthranilic acid: a potent inhibitor of 3-hydroxyanthranilic acid oxidase. Arch. Biochem. Biophys. 2113:161-166.
Perrakis, A., Morris, R., and Lamzin, V. S. 1999. Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6: 458-463.
Pochapsky, T.C., Pochapsky, S.S., Ju,T.T., Mo,H.R, Al-Mjeni, F., Maroney, M.J. 2002.
Modeling and experiment yields the structure of acireductone dioxygenase from Klebsiella pneumoniae. Nature Structural Biology 9: 966 - 972.
Sato, N., Uragami, Y., Nishizaki, T., Takahashi, Y., Sazaki, G., Sugimoto, K., Nonaka, T., Masai, E., Fukuda, M., Senda, T. 2002. Crystal Structures of the Reaction Intermediate and its Homologue of an Extradiol-cleaving Catecholic Dioxygenase. J. Mol. Biol. 321: 621-636.
Schneider, T.R. & Sheldrick, G.M. 2002. Substructure solution with SHELXD. Acta Crystallogr D Biol Crystallogr. 58: 1772-1779.
Schwarcz, R., Okuno, E., White, R.J., Bird, E.D., and Jr. Whetsell, W.O. 1988. 3-Hydroxyanthranilate oxygenase activity is increased in the brains of Huntington disease victims. Proc. Nati Acad. Sci. 85: 4079-4081.
Schwarcz, R., and Pellicciari, R. 2002. Manipulation of Brain Kynurenines: Glial Targets, Neuronal Effects, and Clinical Opportunities. The Journal of pharmacology and experimental therapeutics 303: 1-10.
Schwarcz. R., Whetsell, W.O., Mangano, R.M. 1983. Quinolinic acid: An endogenous metabolite that produces axon-sparing lesions in rat brain. Science 219: 316-318.
Siegbahn, P.E.M., Haeffner, F. 2004. Mechanism for Catechol Ring-Cleavage by Non-Heme Iron Extradiol Dioxygenases. J. AM. CHEM. SOC. 126: 8919-8932.
Solomon, E.I., Brunold, T.C., Davis, M.I., Kemsley, J.N., Lee, S.K., Lehnert, N., Neese, F., Skulan, A J., Yang, Y.S., Zhou, J. 2000. Geometric and Electronic Structure/Function Correlations in Non-Heme Iron Enzymes. Chem.Rev.100: 235-349.
Solomon, E.I., Decker, A., and Lehnert, N. 2003. Non-heme iron enzymes: contrasts to heme catalysis.Proc.Natl. Acad Sci. 100: 3589-3594.
Spence, E.L., Kawamukai, M., Sanvoisin, J., Braven,Helen., and Bugg,T.D. H. 1996 Catechol Dioxygenases from Escherichia coli (MhpB) and Alcaligenes eutrophus (Mpcl): Sequence Analysis and Biochemical Properties of a Third Family of Extradiol Dioxygenases. Journal of Bacteriology. 178: 5249-5256.
Stone. T.W. 2000. Inhibitors of the kynurenine pathway. Eur. J. Med. Chem. 35: 179-186.
Stone, T.W., and Darlington, L.G. 2002. Endogenous kynurenines as targets for drug discovery and development. Nature reviews | Drug dicovery 1: 609-620.
Sugimoto, K., Senda, T., Aoshima, H., Masai, E., Fukuda, M., Fukuda, M., and Mitsui, Y. 1999. Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions. Structure 7: 953-965.
Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
Titus,G.P., Mueller,H.A., Burgner, J., Cordoba, S.R.D., Penalva, M.A. and Timm, D.E. 2000 Crystal structure of human homogentisate dioxygenase. nature structural biology 7: 542-546.
Vaillancourt, F. H., Barbosa, C. J., Spiro, T. G., Bolin, J. T., Blades, M. W., Turner, R. F., and Eltis, L. D. 2002. Definitive evidence for monoanionic binding of 2,3-dihydroxybiphenyl to 2,3-dihydroxybiphenyl 1,2-dioxygenase from UV resonance Raman spectroscopy, UV/Vis absorption spectroscopy, and crystallography, J. Am. Chem. Soc. 124: 2485-96.
Viggiani, A., Siani, L., Notomista, E., Biroio, L, Pucci, P., and Donato. A. D. 2004. The Role of the Conserved Residues His-246, His-199, and Tyr-255 in the Catalysis of Catechol 2,3-Dioxygenase from Pseudomonas stutzeri OXl. The Journal of Biological Chemistry. 279: 48630-48639.
Vetting, M.W., Wackett, L.P., Jr. Que, L., Lipscomb, J.D., Ohlendorf, D.H. 2004. Crystallographic Comparison of Manganese- and Iron-Dependent Homoprotocatechuate 2,3-Dioxygenases. Journal of Bacteriology. 186: 1945-1958.
Walsh, J.L., Wu, H.Q., Ungerstedt, U., and Schwarcz, R. 1994. 4-Chloro-3-hydroxyanthranilate inhibits quinolinate production in the rat hippocampus in vivo. Brain Res. Bull. 33: 513-516.
Woo, E.J., Dunwell, J. M., Goodenough, P. W., Marvier, A. C, and Pickersgill,R.W. 2000 Germin is a manganese containing homohexamer with oxalate oxidase and superoxide dismutase Activitie. Nature Structural Biology 7: 1036 - 1040.
Woo, E.J., Marshall, J., Bauly, J., Chen, J.G., Venis, M., Napier, R.M., Pickersgill, R.W. 2002. Crystal structure of auxin-binding protein 1 in complex with auxin. 21: 2877-2885.
Zhang, Y., Colabroy, K.L., Begley, T.P., and Ealick, S.E. 2005. Structural Studies on 3-Hydroxyanthranilate-3,4-dioxygenase: The Catalytic Mechanism of a Complex Oxidation Involved in NAD Biosynthesis. Biochemistry 44: 7632-7643.
Ahmed, M., Taylor, W., Smith, P.R., and Becker, M. A. 1999. Accelerated Transcription of PRPS1 in X-linked Overactivity of Normal Human Phosphoribosylpyrophosphate Synthetase. THE JOURNAL OF BIOLOGICAL CHEMISTRY 274:7482-7488.
Becker, M.A., Smith, P.R., Taylor, W., Mustafi, R., and Switzert, R.L. 1995. The Genetic and Functional Basis of Purine Nucleotide Feedback-resistant Phosphoribosylpyrophosphate Synthetase Superactivity. J. Clin. Invest. 96:2133-2141.
Becker, M.A., Taylor, W., Smith, P.R., and Ahmed, M. 1996. Overexpression of the Normal Phosphoribosylpyrophosphate Synthetase 1 Isoform Underlies Catalytic Superactivity of Human Phosphoribosylpyrophosphate Synthetase. THE JOURNAL OF BIOLOGICAL CHEMISTRY 271: 19894-19899.
Eriksen,T.A., Kadziola, A., Bentsen, A.K.,Harlow, K.W., and Larsen, S. 2000.
Structural basis for the function of Bacillus subtilis phosphoribosylpyrophosphate Synthetase. nature structural biology 7: 303-308.
Eriksen, T.A., Kadziola, A., and Larsen, S. 2002. Binding of cations in Bacillus subtilis phosphoribosyldiphosphate synthetase and their role in catalysis. Protein Science 11:271-279.
Garcr'a-Pavr'a, P., Torres, R.J., Rivero, M., Ahmed, M., Garcr'a-Puig, J., and Becket, M.A. 2003.
Phosphoribosylpyrophosphate Synthetase Overactivity as a Cause of Uric Acid Overproduction in a Young Woman. ARTHRITIS & RHEUMATISM 48:2036-2041.
Kadziola, A., Jepsen, C.H., Johansson, E., McGuire, J., Larsen, S., and Hove-Jensen, B. 2005.
Novel Class Ⅲ Phosphoribosyl Diphosphate Synthase: Structure and Properties of the Tetrameric, Phosphateactivated, Non-allosterically Inhibited Enzyme from Methanocaldococcus jannaschii. J. Mol. Biol. 354: 815-828.
Burger, A.M., and Seth, A.K. 2004. The ubiquitin-mediated protein degradation pathway in cancer: therapeutic implications. European Journal of Cancer 40: 2217-2229.
Cook, W.J., Jeffrey, L.C., Xu, Y., and Chau, V. 1993 Tertiary structures of class 1 ubiquitin-conjugating enzymes are highly conserved: crystal structure of yeast Ubc4. Biochemistry 32: 13809-13817.
Glickman, M.H., and Ciechanover, A. 2002.The Ubiquitin-Proteasome Proteolytic Pathway: Destruction for the Sake of Construction. Physiol Rev 82: 373-428.
Itol, K., Adachil, S., Iwakami, R., Yasuda, H., Muto, Y., Seki, N., and Okanol, Y. 2001.
N-Terminally extended human ubiquitin-conjugating enzymes (E2s) mediate the ubiquitination of RING-finger proteins, ARA54 and RNF8. Eur. J. Biochem. 268: 2725-2732.
Nuber, U., Schwarz, S., Kaiser, P., Schneider,R., and Scheffner, M. 1995. Cloning of Human Ubiquitin-conjugating Enzymes UbcH6 and UbcH7(E2-Fl) and Characterization of Their Interaction with E6-AP and RSP5. The Journal of Biological Chemistry 271: 2795-2800.
Anand, R., Dorrestein, P.C., Kinsland, C, Begley, T. P., and Ealick, S.E. 2002. Structure of Oxalate Decarboxylase from Bacillus subtilis at 1.75 A Resolution. Biochemistry 41: 7659-7669.
Bassan, A., Borowski T., and Siegbahn. P.E.M. 2004. Quantum chemical studies of dioxygen activation by mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad. DaltonTrans 2004: 3153-3162.
Brunger, A. T., et al. 1998. Crystallography and N. M. R. system: a new software suite for macromolecular structure determination. Acta Cystallogr. D 54, 905-921.
Bugg, T. D. H., and Lin, G. 2001. Solving the riddle of the intradiol and extradiol catechol dioxygenases: how do enzymes control hydroperoxide rearrangements? Chem. Commun. 941-952.
Bugg, T. D., Sanvoisin, J., Spence, E. L. 1997. Exploring the catalytic mechanism of the extradiol catechol dioxygenases. Biochem. Soc. Trans.25: 81-85.
Calderone, V., Trabucco, M, Menin, V., Negro, A. 2002. Cloning of human 3-hydroxyanthranilic acid dioxygenase in Escherichia coli: characterisation of the purified enzyme and its in vitro inhibition by Zn~(2+) . Biochimica et Biophysica Acta 1596: 283-292.
Cleasby, A., Wonacott, A., Skarzynski, T., Hubbard, R.E., Davies, G.J., Proudfoot, A.E., Bernard, A.R., Payton, M.A., Wells, T.N. 1996. The x-ray crystal structure of phosphomannose isomerase from Candida albicans at 1.7 angstrom resolution. Nat Struct Biol. 3: 470-9.
Colabroy, K. L., Zhai, H., Li, T., Ge, Y., Zhang, Y., Liu, A., Ealick, S.E., McLafferty, F.W., Begley, T.P. 2005. The Mechanism of Inactivation of 3-Hydroxyanthranilate-3,4-dioxygenase by 4-Chloro-3-hydroxyanthranilate, Biochemistry 44: 7623-7631.
Costas, M., Mehn, M.P., Jensen, M.P., Jr. Que, L. 2004. Dioxygen Activation at Mononuclear Nonheme Iron Active Sites: Enzymes, Models, and Intermediates., Jr. Chem.Rev. 104: 936-986.
Cowtan, K. 1999. Error estimation and bias correction in phase-improvement calculations. Acta Crystallogr. D. Biol. Crystallogr. 55: 1555-1567.
Dunwell, J.M., Culham, A., Carter, C.E., Sosa-Aguirre, C.R., and Goodenough, P.W. 2001. Evolution of functional diversity in the cupin superfamily. TRENDS in Biochemical Sciences 26:740-746.
Dunwell, J.M., Purvis, A., Khuri, S. 2004. Cupins: the most functionally diverse protein superfamily? Phytochemistry 65: 7-17.
Fritze, I.M., Linden, L., Freigang, J., Auerbach, G., Huber, R., and Steinbacher, S. 2004. The Crystal Structures of Zea mays and Arabidopsis 4-Hydroxyphenylpyruvate Dioxygenase. Plant Physiology 134: 1388-1400.
Gerlt, J.A., Babbitt, P.C. 2001.DIVERGENT EVOLUTION OF ENZYMATIC FUNCTION: Mechanistically Diverse Superfamilies and Functionally Distinct Suprafamilies. 70: 209-246.
Gopal, B., Madan, L.L. Betz, S.F. and Kossiakoff, A.A. 2005. The Crystal Structure of a Quercetin 2,3-Dioxygenase from Bacillus subtilis Suggests Modulation of Enzyme Activity by a Change in the Metal Ion at the Active Site(s). Biochemistry 44: 193-201.
Gouet, P., Courcelle, E., Stuart, D.I., and Metoz, F. 1999. ESPript: Multiple sequence alignments in PostScript. Bioinformatics 15: 305-308.
Guidetti, P., Luthi-Carter, R.E., Augood, S.J., and Schwarcz, R. 2004. Neostriatal and cortical quinolinate levels are increased in early grade Huntington's disease. Neurobiology of Disease 17: 455-461.
Hasegawa, Y., Muraki, T., Tokuyama,T., Iwaki, H., Tatsuno, M., Lau, P.C.K. 2000. A novel degradative pathway of 2-nitrobenzoate via 3-hydroxyanthranilate in Pseudomonas fuorescens strain K.U-7. FEMS Microbiology Letter 190: 185-190.
Heyes, M.P., Achim, C.L., Wiley, C.A., Major,E.O., Saito, K., and Markey, S.P. 1996.
Human microglia convert L-tryptophan into the neurotoxin quinolinic acid. biochem.J. 320: 595-597.
Heyes, M. P., Saito, K., Jacobowitz, D., Markey, S. P., Takikawa, O., and Vickers, J. H. 1992. Poliovirus induces indoleamine-2,3-dioxygenase and quinolinic acid synthesis in macaque brain. FASEB J. 6: 2977-89.
Koehntop, K.D., Emerson, J.P., and Jr Que, L. 2005. The 2-His-1-carboxylate facial triad: a versatile platform for dioxygen activation by mononuclear non-heme iron(II) enzymes. Journal of Biological Inorganic Chemistry 10: 87-93.
Koontz, W.A., and Shiman, R. 1976. Beef Kidney 3-Hydroxyanthranilic Acid Oxygenase PURIFICATION, CHARACTERIZATION, AND ANALYSIS OF THE ASSAY J. Biol. Chem. 251: 368-377.
Kucharczyka, R., Zagulskia, M, Rytkaa, J., Herbertb, C.J. 1998. The yeast gene YJR025c encodes a 3-hydroxyanthranilic acid dioxygenase and is involved in nicotinic acid biosynthesis. FEBS Letters 424: 127-130.
Kurnasov, O., Goral, V., Colabroy, K., Gerdes, S., Anantha, S., Osterman, A., and Begley, T. P. 2003. NAD biosynthesis: identification of the tryptophan to quinolinate pathway in bacteria.Chem . Biol. 10: 1195-204.
La Fortelle, E. de, Irwin, J.J., and Bricogne, G. 1997. SHARP: A maximum-likelihood heavy-atom parameter refinement and phasing program for the MIR and MAD methods. In Crystallographic computing (eds. P. Bourne and K. Watenpaugh), pp. 250-262. IUCR, Oxford, UK.
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.
Lendenmann, U., Spain, J.C. 1996. 2-Aminophenol 1,6-Dioxygenase: a Novel Aromatic Ring Cleavage Enzyme Purified from Pseudomonas pseudoalcaligenes JS45. Journal of Bacteriolog. 178:6227-6232.
Malherbe, P, Koehler, C, Da Prada, M., Lang, G., Kiefer, V., Schwarcz, R., Lahm, H.-W., and Cesura, A. M. 1994. Molecular cloning and functional expression of human 3-hydroxyanthranilicacid dioxygenase,.J Biol. Chem. 269:13792-7.
Matthews, B.W. 1968. Solvent content of protein crystals. J. Mol. Biol. 33: 491-497.
Mendel, S., Arndt,A., and Bugg, T. D. H. 2004. Acid-Base Catalysis in the Extradiol Catechol Dioxygenase Reaction Mechanism: Site-Directed Mutagenesis of His-115 and His-179 in Escherichia coli 2,3-Dihydroxyphenylpropionate 1,2-Dioxygenase (MhpB). Biochemistry 43: 13390-13396.
Mitchell,R.A.,Kang,H.H.,and Henderson, L.M. 1963. Inactivation during Functioning of 3-Hydroxyanthranilate Oxidase Resulting from Oxidation of Bound Ferrous Iron. J. Biol. Chem. 238: 1151-1155.
Muraki,T., Taki, M.. Hasegawa, Y.. Iwaki, H., Lau, P.C.K. 2003. Prokaryotic Homologs of the Eukaryotic 3-Hydroxyanthranilate 3,4-Dioxygenase and 2-Amino-3-Carboxymuconate-6-Semialdehyde Decarboxylase in the 2-Nitrobenzoate Degradation Pathway of Pseudomonas fluorescens Strain KU-7. Applid And Environmental Microbiology 69:1564-1572.
Murakami,S., Sawami, Y., Takenaka, S., and Aoki,K. 2004 Cloning of a gene encoding 4-amino-3-hydroxybenzoate 2,3-dioxygenase from Bordetella sp. 10d. Biochemical and Biophysical Research Communications 314: 489-494.
Murshudov. G.N., Vagin, A.A., Dodson. E.J. (1997). Refinement of Macromolecular Structures by the Maximum-Likelihood Method. Acta Cryst. D53: 240-255.
Murzin,A.G., Brenner,S.E., Hubbard.T., Chothia,C. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures.J. Mol. Biol. 247:536-540.
Nandi, D., Lightcap, E.S., Koo, Y. K., Lu, X.L., Quancard, J., Silverman, R.B. 2003. Purification and inactivation of 3-hydroxyanthranilic acid 3,4-dioxygenase from beef liver. The International Journal of Biochemistry & Cell Biology 35: 1085-1097.
Nogales, J., Canales, A., Jimenez-Barbero, J., Garcia, J. L., and Diaz, E. 2005.
Molecular Characterization of the Gallate Dioxygenase from Pseudomonas putida KT2440: the Prototype of a New Subgroup of Extradiol Dioxygenases. J. Biol. Chem.280: 35382-90.
Otwinowski, Z. and Minor, W. 1997. Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276A: 307-326.
Pandey, J., Paul. D,, Jain, R.K. 2003. Branching of o-nitrobenzoate degradation pathway in Arthrobacter protophormiae RKJ 100: identification of new intermediates. FEMS Microbiology Letters 229:231-236,
Parli, C.J., Krieter, P., and Schmidt, B. 1980. Metabolism of 6-chlorotryptophan to 4-chloro-3-hydroxyanthranilic acid: a potent inhibitor of 3-hydroxyanthranilic acid oxidase. Arch. Biochem. Biophys. 2113:161-166.
Perrakis, A., Morris, R., and Lamzin, V. S. 1999. Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6: 458-463.
Pochapsky, T.C., Pochapsky, S.S., Ju,T.T., Mo,H.R, Al-Mjeni, F., Maroney, M.J. 2002.
Modeling and experiment yields the structure of acireductone dioxygenase from Klebsiella pneumoniae. Nature Structural Biology 9: 966 - 972.
Sato, N., Uragami, Y., Nishizaki, T., Takahashi, Y., Sazaki, G., Sugimoto, K., Nonaka, T., Masai, E., Fukuda, M., Senda, T. 2002. Crystal Structures of the Reaction Intermediate and its Homologue of an Extradiol-cleaving Catecholic Dioxygenase. J. Mol. Biol. 321: 621-636.
Schneider, T.R. & Sheldrick, G.M. 2002. Substructure solution with SHELXD. Acta Crystallogr D Biol Crystallogr. 58: 1772-1779.
Schwarcz, R., Okuno, E., White, R.J., Bird, E.D., and Jr. Whetsell, W.O. 1988. 3-Hydroxyanthranilate oxygenase activity is increased in the brains of Huntington disease victims. Proc. Nati Acad. Sci. 85: 4079-4081.
Schwarcz, R., and Pellicciari, R. 2002. Manipulation of Brain Kynurenines: Glial Targets, Neuronal Effects, and Clinical Opportunities. The Journal of pharmacology and experimental therapeutics 303: 1-10.
Schwarcz. R., Whetsell, W.O., Mangano, R.M. 1983. Quinolinic acid: An endogenous metabolite that produces axon-sparing lesions in rat brain. Science 219: 316-318.
Siegbahn, P.E.M., Haeffner, F. 2004. Mechanism for Catechol Ring-Cleavage by Non-Heme Iron Extradiol Dioxygenases. J. AM. CHEM. SOC. 126: 8919-8932.
Solomon, E.I., Brunold, T.C., Davis, M.I., Kemsley, J.N., Lee, S.K., Lehnert, N., Neese, F., Skulan, A J., Yang, Y.S., Zhou, J. 2000. Geometric and Electronic Structure/Function Correlations in Non-Heme Iron Enzymes. Chem.Rev.100: 235-349.
Solomon, E.I., Decker, A., and Lehnert, N. 2003. Non-heme iron enzymes: contrasts to heme catalysis.Proc.Natl. Acad Sci. 100: 3589-3594.
Spence, E.L., Kawamukai, M., Sanvoisin, J., Braven,Helen., and Bugg,T.D. H. 1996 Catechol Dioxygenases from Escherichia coli (MhpB) and Alcaligenes eutrophus (Mpcl): Sequence Analysis and Biochemical Properties of a Third Family of Extradiol Dioxygenases. Journal of Bacteriology. 178: 5249-5256.
Stone. T.W. 2000. Inhibitors of the kynurenine pathway. Eur. J. Med. Chem. 35: 179-186.
Stone, T.W., and Darlington, L.G. 2002. Endogenous kynurenines as targets for drug discovery and development. Nature reviews | Drug dicovery 1: 609-620.
Sugimoto, K., Senda, T., Aoshima, H., Masai, E., Fukuda, M., Fukuda, M., and Mitsui, Y. 1999. Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions. Structure 7: 953-965.
Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
Titus,G.P., Mueller,H.A., Burgner, J., Cordoba, S.R.D., Penalva, M.A. and Timm, D.E. 2000 Crystal structure of human homogentisate dioxygenase. nature structural biology 7: 542-546.
Vaillancourt, F. H., Barbosa, C. J., Spiro, T. G., Bolin, J. T., Blades, M. W., Turner, R. F., and Eltis, L. D. 2002. Definitive evidence for monoanionic binding of 2,3-dihydroxybiphenyl to 2,3-dihydroxybiphenyl 1,2-dioxygenase from UV resonance Raman spectroscopy, UV/Vis absorption spectroscopy, and crystallography, J. Am. Chem. Soc. 124: 2485-96.
Viggiani, A., Siani, L., Notomista, E., Biroio, L, Pucci, P., and Donato. A. D. 2004. The Role of the Conserved Residues His-246, His-199, and Tyr-255 in the Catalysis of Catechol 2,3-Dioxygenase from Pseudomonas stutzeri OXl. The Journal of Biological Chemistry. 279: 48630-48639.
Vetting, M.W., Wackett, L.P., Jr. Que, L., Lipscomb, J.D., Ohlendorf, D.H. 2004. Crystallographic Comparison of Manganese- and Iron-Dependent Homoprotocatechuate 2,3-Dioxygenases. Journal of Bacteriology. 186: 1945-1958.
Walsh, J.L., Wu, H.Q., Ungerstedt, U., and Schwarcz, R. 1994. 4-Chloro-3-hydroxyanthranilate inhibits quinolinate production in the rat hippocampus in vivo. Brain Res. Bull. 33: 513-516.
Woo, E.J., Dunwell, J. M., Goodenough, P. W., Marvier, A. C, and Pickersgill,R.W. 2000 Germin is a manganese containing homohexamer with oxalate oxidase and superoxide dismutase Activitie. Nature Structural Biology 7: 1036 - 1040.
Woo, E.J., Marshall, J., Bauly, J., Chen, J.G., Venis, M., Napier, R.M., Pickersgill, R.W. 2002. Crystal structure of auxin-binding protein 1 in complex with auxin. 21: 2877-2885.
Zhang, Y., Colabroy, K.L., Begley, T.P., and Ealick, S.E. 2005. Structural Studies on 3-Hydroxyanthranilate-3,4-dioxygenase: The Catalytic Mechanism of a Complex Oxidation Involved in NAD Biosynthesis. Biochemistry 44: 7632-7643.
Ahmed, M., Taylor, W., Smith, P.R., and Becker, M. A. 1999. Accelerated Transcription of PRPS1 in X-linked Overactivity of Normal Human Phosphoribosylpyrophosphate Synthetase. THE JOURNAL OF BIOLOGICAL CHEMISTRY 274:7482-7488.
Becker, M.A., Smith, P.R., Taylor, W., Mustafi, R., and Switzert, R.L. 1995. The Genetic and Functional Basis of Purine Nucleotide Feedback-resistant Phosphoribosylpyrophosphate Synthetase Superactivity. J. Clin. Invest. 96:2133-2141.
Becker, M.A., Taylor, W., Smith, P.R., and Ahmed, M. 1996. Overexpression of the Normal Phosphoribosylpyrophosphate Synthetase 1 Isoform Underlies Catalytic Superactivity of Human Phosphoribosylpyrophosphate Synthetase. THE JOURNAL OF BIOLOGICAL CHEMISTRY 271: 19894-19899.
Eriksen,T.A., Kadziola, A., Bentsen, A.K.,Harlow, K.W., and Larsen, S. 2000.
Structural basis for the function of Bacillus subtilis phosphoribosylpyrophosphate Synthetase. nature structural biology 7: 303-308.
Eriksen, T.A., Kadziola, A., and Larsen, S. 2002. Binding of cations in Bacillus subtilis phosphoribosyldiphosphate synthetase and their role in catalysis. Protein Science 11:271-279.
Garcr'a-Pavr'a, P., Torres, R.J., Rivero, M., Ahmed, M., Garcr'a-Puig, J., and Becket, M.A. 2003.
Phosphoribosylpyrophosphate Synthetase Overactivity as a Cause of Uric Acid Overproduction in a Young Woman. ARTHRITIS & RHEUMATISM 48:2036-2041.
Kadziola, A., Jepsen, C.H., Johansson, E., McGuire, J., Larsen, S., and Hove-Jensen, B. 2005.
Novel Class Ⅲ Phosphoribosyl Diphosphate Synthase: Structure and Properties of the Tetrameric, Phosphateactivated, Non-allosterically Inhibited Enzyme from Methanocaldococcus jannaschii. J. Mol. Biol. 354: 815-828.
Burger, A.M., and Seth, A.K. 2004. The ubiquitin-mediated protein degradation pathway in cancer: therapeutic implications. European Journal of Cancer 40: 2217-2229.
Cook, W.J., Jeffrey, L.C., Xu, Y., and Chau, V. 1993 Tertiary structures of class 1 ubiquitin-conjugating enzymes are highly conserved: crystal structure of yeast Ubc4. Biochemistry 32: 13809-13817.
Glickman, M.H., and Ciechanover, A. 2002.The Ubiquitin-Proteasome Proteolytic Pathway: Destruction for the Sake of Construction. Physiol Rev 82: 373-428.
Itol, K., Adachil, S., Iwakami, R., Yasuda, H., Muto, Y., Seki, N., and Okanol, Y. 2001.
N-Terminally extended human ubiquitin-conjugating enzymes (E2s) mediate the ubiquitination of RING-finger proteins, ARA54 and RNF8. Eur. J. Biochem. 268: 2725-2732.
Nuber, U., Schwarz, S., Kaiser, P., Schneider,R., and Scheffner, M. 1995. Cloning of Human Ubiquitin-conjugating Enzymes UbcH6 and UbcH7(E2-Fl) and Characterization of Their Interaction with E6-AP and RSP5. The Journal of Biological Chemistry 271: 2795-2800.