来源于人的硫脂酶超家族成员2以及晶状体蛋白Mu crystallin的晶体结构以及生物学功能研究
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摘要
人源硫酯酶超家族成员2(hTHEM2)在我们研究之前只是一个假想蛋白，对于其功能和结构一无所知。我们在结构基因组的项目支持下，首次克隆了该基因，并且在大肠杆菌中过量的表达，纯化，结晶该蛋白，并且利用Se-SAD法成功的解析了该蛋白2.3埃的晶体结构。晶体结构解析出之后，我们根据其结构与国外合作进行了其酶底物的筛选。为了了解其细胞内的功能，我们制备了该蛋白的单克隆抗体，同时也利用RT-PCR的方法检查了该蛋白在小鼠12种组织中的组织表达特异性，利用绿色荧光融合蛋白和免疫荧光的方法在两种癌细胞系中进行了其细胞内的定位，利用基于载体的siRNA敲减技术在HCT116细胞系中成功的对该基因进行了敲减。
人源硫酯酶超家族成员2的晶体结构显示该蛋白属于‘热狗’折叠模式，即六个β折叠片包裹着一个长的α螺旋。通过DALI搜索，我们发现该蛋白结构和来源于大肠杆菌的苯乙酸降解途径中的PaaI的结构非常相似，底物筛选的结果显示出与大肠杆菌PAAI具有相同的底物特异性：都可以水解苯环氧化的苯乙酸辅酶A生成苯环氧化的苯乙酸以及辅酶A，但是其催化效率却只有大肠杆菌的百分之一。位于中心α螺旋的上的残基Asp65，通过单点突变实验证明该位点是催化反应所必须的。
通过RT-PCR在小鼠中的组织表达特异性表明，该蛋白在肾脏中有大量的表达，同时在大肠，小肠，脑，前列腺，子宫，睾丸中都有表达，而在胃中没有检测到有表达。关于细胞内的定位，利用两种独立的方法，即绿色荧光融合蛋白以及免疫荧光的方法都检测到该蛋白可能结合在微管上面。当细胞进入分裂期后，该蛋白的分布明显呈现出纺锤体的分布模式，利用免疫荧光的方法与β-tubulin的共定位实验证明该蛋白和微管蛋白是共定位的。通过siRNA敲减的细胞克隆形成实验证明，hTHEM2的敲减可以抑制癌细胞HCT116的生长。
来源于人的P38细胞质T3结合蛋白，也叫做Mu_crystallin，在把甲状腺素T3从细胞质转运到细胞核以及在调控甲状腺荷尔蒙相关基因的表达方面起到非常重要的作用。我们利用悬滴法获得了该蛋白的单晶，并且在室内X光源上收集到一套2.6埃的晶体数据。使用分子置换法成功解析了相位并最终修正到2.6埃。晶体结构显示该蛋白可以分为两个结构域：二体化结构域以及NADPH结合结构域。分析发现不对称单位中的两个分子中的Pro90具有顺反异构的现象。通过与同源蛋白的结构比较我们提出了Mu crystallin与T3的结合模型。
Human thioesterase superfamily member 2 (hTHEM2) belongs to the hotdog-fold enzyme superfamily but its biological function remains unknown. Tissue specific expression in mouse showed that the encoding gene is highly expressed in the kidney. and moderately expressed in the liver, brain, large intestine and small intestine. Small interference RNA silencing in cell line HCT116 shows that the hthem2 gene is essential for the cell sustained proliferation. Immunostaining and GFP-Tag experiments show that hTHEM2 is co-localized with microtubules.
Since hTHEM2 exhibits about 20% sequence identity to Escherichia coli PaaI protein, it was proposed to be a thioesterase with a hotdog-fold. We describe the crystallographic structure of recombinant hTHEM2, determined by the single-wavelength anomalous dispersion method at 2.3 A resolution. This structure demonstrates that hTHEM2 indeed contains a hotdog-fold and forms a back-to-back tetramer as other hotdog proteins. Based on structural and sequence conservation, the thioesterase active site in hTHEM2 is predicted. The structure and substrate specificity are most similar to those of the bacterial phenylacetyl-CoA hydrolase. Asp65, located on the central α-helix of subunit B, was shown by site-directed mutagenesis to be essential to catalysis.
Human cytosolic 3,5,3'-triiodo-L-thyronine-binding protein, also called Mu_crystallin or CRYM, plays important physiological roles in transporting 3,5,3'-triiodo-L-thyronine (T3) into nuclei and regulating thyroid hormone related gene expression. We report crystal structure of human CRYM bound with NADPH. The structure contains two domains: a Rossemann fold like NADPH binding domain and a dimerization domain. Different conformations of the loop Arg83-His92 have been observed in two monomers of human CRYM in the same asymmetric unit. The peptide bond of Val89-Pro90 is a trans-configuration in one monomer but a cis-configuration in the other. Finally, a putative T3-binding site in human CRYM is proposed based on comparison with other structural homologues.
人源硫酯酶超家族成员2的晶体结构显示该蛋白属于‘热狗’折叠模式，即六个β折叠片包裹着一个长的α螺旋。通过DALI搜索，我们发现该蛋白结构和来源于大肠杆菌的苯乙酸降解途径中的PaaI的结构非常相似，底物筛选的结果显示出与大肠杆菌PAAI具有相同的底物特异性：都可以水解苯环氧化的苯乙酸辅酶A生成苯环氧化的苯乙酸以及辅酶A，但是其催化效率却只有大肠杆菌的百分之一。位于中心α螺旋的上的残基Asp65，通过单点突变实验证明该位点是催化反应所必须的。
通过RT-PCR在小鼠中的组织表达特异性表明，该蛋白在肾脏中有大量的表达，同时在大肠，小肠，脑，前列腺，子宫，睾丸中都有表达，而在胃中没有检测到有表达。关于细胞内的定位，利用两种独立的方法，即绿色荧光融合蛋白以及免疫荧光的方法都检测到该蛋白可能结合在微管上面。当细胞进入分裂期后，该蛋白的分布明显呈现出纺锤体的分布模式，利用免疫荧光的方法与β-tubulin的共定位实验证明该蛋白和微管蛋白是共定位的。通过siRNA敲减的细胞克隆形成实验证明，hTHEM2的敲减可以抑制癌细胞HCT116的生长。
来源于人的P38细胞质T3结合蛋白，也叫做Mu_crystallin，在把甲状腺素T3从细胞质转运到细胞核以及在调控甲状腺荷尔蒙相关基因的表达方面起到非常重要的作用。我们利用悬滴法获得了该蛋白的单晶，并且在室内X光源上收集到一套2.6埃的晶体数据。使用分子置换法成功解析了相位并最终修正到2.6埃。晶体结构显示该蛋白可以分为两个结构域：二体化结构域以及NADPH结合结构域。分析发现不对称单位中的两个分子中的Pro90具有顺反异构的现象。通过与同源蛋白的结构比较我们提出了Mu crystallin与T3的结合模型。
Human thioesterase superfamily member 2 (hTHEM2) belongs to the hotdog-fold enzyme superfamily but its biological function remains unknown. Tissue specific expression in mouse showed that the encoding gene is highly expressed in the kidney. and moderately expressed in the liver, brain, large intestine and small intestine. Small interference RNA silencing in cell line HCT116 shows that the hthem2 gene is essential for the cell sustained proliferation. Immunostaining and GFP-Tag experiments show that hTHEM2 is co-localized with microtubules.
Since hTHEM2 exhibits about 20% sequence identity to Escherichia coli PaaI protein, it was proposed to be a thioesterase with a hotdog-fold. We describe the crystallographic structure of recombinant hTHEM2, determined by the single-wavelength anomalous dispersion method at 2.3 A resolution. This structure demonstrates that hTHEM2 indeed contains a hotdog-fold and forms a back-to-back tetramer as other hotdog proteins. Based on structural and sequence conservation, the thioesterase active site in hTHEM2 is predicted. The structure and substrate specificity are most similar to those of the bacterial phenylacetyl-CoA hydrolase. Asp65, located on the central α-helix of subunit B, was shown by site-directed mutagenesis to be essential to catalysis.
Human cytosolic 3,5,3'-triiodo-L-thyronine-binding protein, also called Mu_crystallin or CRYM, plays important physiological roles in transporting 3,5,3'-triiodo-L-thyronine (T3) into nuclei and regulating thyroid hormone related gene expression. We report crystal structure of human CRYM bound with NADPH. The structure contains two domains: a Rossemann fold like NADPH binding domain and a dimerization domain. Different conformations of the loop Arg83-His92 have been observed in two monomers of human CRYM in the same asymmetric unit. The peptide bond of Val89-Pro90 is a trans-configuration in one monomer but a cis-configuration in the other. Finally, a putative T3-binding site in human CRYM is proposed based on comparison with other structural homologues.
引文
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Cohen, G. B., V. S. Rangan, et al. (2000). "The human thioesterase II protein binds to a site on HIV-1 Nef critical for CD4 down-regulation." J Biol Chem 275(30): 23097-105.
Dillon, S. C. and A. Bateman (2004). "The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases." BMC Bioinformatics 5(1): 109.
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Ferrandez, A., B. Minambres, et al. (1998). "Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway." J Biol Chem 273(40): 25974-86.
Gouet, P., E. Courcelle, et al. (1999). "ESPript: analysis of multiple sequence alignments in PostScript." Bioinformatics 15(4): 305-8.
Halford, W. P. (1999). "The essential prerequisites for quantitative RT-PCR." Nat Biotechnol 17(9): 835.
Hanna, Z., Kay, D. G., Rebai, N., Guimond, A., Jothy, S. & Jolicoeur, P. (1998). "Nef harbors a major determinant of pathogenicity for an AIDS-like disease induced by HIV-1 in transgenic mice." Cell 95: 163-175.
Holm, L. and C. Sander (1993). "Protein structure comparison by alignment of distance matrices.".J Mol Biol 233(1): 123-38.
Jones, T. A., J. Y. Zou, et al. (1991). "Improved methods for building protein models in electron density maps and the location of errors in these models." Acta Crystallogr A 47 ( Pt 2): 110-9.
Kabsch, W. and C. Sander (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features." Biopolymers 22(12): 2577-637.
Kunishima, N., Y. Asada, et al. (2005). "A novel induced-fit reaction mechanism of asymmetric hot dog thioesterase PAAI." J Mol Biol 352(1): 212-28.
Li, J., U. Derewenda, et al. (2000). "Crystal structure of the Escherichia coil thioesterase Ⅱ, a homolog of the human Nef binding enzyme." Nat Struct Biol 7(7): 555-9.
Marone, M., S. Mozzetti, et al. (2001). "Semiquantitative RT-PCR analysis to assess the expression levels of multiple transcripts from the same sample." B iol Proced Online 3:19-25.
Meadus, W. J. (2003). "A semi-quantitative RT-PCR method to measure the in vivo effect of dietary conjugated linoleic acid on porcine muscle PPAR gene expression." Biol Proced Online 5: 20-28.
Olivera, E. R., B. Minambres, et al. (1998). "Molecular characterization of the phenylacetic acid catabolic pathway in Pseudomonas putida U: the phenylacetyl-CoA catabolon." Proc Natl Acad Sci U S A 95(11): 6419-24.
Schneider, T. R. and G. M. Sheidrick (2002). "Substructure solution with SHELXD." Acta Crystallogr D Biol Crystallogr 58(Pt 10 Pt 2): 1772-9.
Song, F., Zhuang, Z., Lorenzo Finci, Debra Dunaway-Mariano; Ryan Kniewel, John A. Buglino, Veronica Solorzano, Jin Wu, and Christopher D. Lima. (2006). "Structure, function and mechanism of the phenylacetate pathway hotdog-fold thioesterase Paal." Journal of Biological Chemistry.
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Terwilliger, T. C. (2002). "Rapid automatic NCS identification using heavy-atom substructures." Acta Crystallogr D Biol Crystallogr 58(Pt 12): 2213-5.
Vie, M. P., C. Evrard, et al. (1997). "Purification, molecular cloning, and functional expression of the human nicodinamide-adenine dinucleotide phosphate-regulated thyroid hormone-binding protein." Mol Endocrinol 11(11): 1728-36.
Wael Ismail, M. E.-S. M., Barry L. Wanner, Kirill A. Datsenko, Woifgang Eisenreich,Felix Rohdich, Adelbert Bacher and Georg Fuchs (2003). "Functional genomics by NMR spectroscopy Phenylacetate catabolism in Escherichia coli." Eur. J. Biochem 270: 3047-3054.
Abe, S., T. Katagiri, et al. (2003). "Identification of CRYM as a candidate responsible for nonsyndromic deafness, through cDNA microarray analysis of human cochlear and vestibular tissues." Am J Hum Genet 72(1): 73-82.
Apriletti, J. W., J. D. Baxter, et al. (1995). "Expression of the rat alpha 1 thyroid hormone receptor ligand binding domain in Escherichia coli and the use of a ligand-induced conformation change as a method for its purification to homogeneity." Protein Expr Purif 6(3): 363-70.
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Cohen, G. B., V. S. Rangan, et al. (2000). "The human thioesterase II protein binds to a site on HIV-1 Nef critical for CD4 down-regulation." J Biol Chem 275(30): 23097-105.
Dillon, S. C. and A. Bateman (2004). "The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases." BMC Bioinformatics 5(1): 109.
Dunaway-Mariano D, B. P. (1994). "On the origins and functions of the enzymes of the 4-chlorobenzoate to 4-hydroxybenzoate converting pathway." Biodegradation 5: 259-276.
EDUARDO DI'AZ, A. F. N., MARI'A A. PRIETO, AND JOSE'L. GARCI'A (2001). "Biodegradation of Aromatic Compounds by Escherichia coli." MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS: 523-569.
Ferrandez, A., B. Minambres, et al. (1998). "Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway." J Biol Chem 273(40): 25974-86.
Gouet, P., E. Courcelle, et al. (1999). "ESPript: analysis of multiple sequence alignments in PostScript." Bioinformatics 15(4): 305-8.
Halford, W. P. (1999). "The essential prerequisites for quantitative RT-PCR." Nat Biotechnol 17(9): 835.
Hanna, Z., Kay, D. G., Rebai, N., Guimond, A., Jothy, S. & Jolicoeur, P. (1998). "Nef harbors a major determinant of pathogenicity for an AIDS-like disease induced by HIV-1 in transgenic mice." Cell 95: 163-175.
Holm, L. and C. Sander (1993). "Protein structure comparison by alignment of distance matrices.".J Mol Biol 233(1): 123-38.
Jones, T. A., J. Y. Zou, et al. (1991). "Improved methods for building protein models in electron density maps and the location of errors in these models." Acta Crystallogr A 47 ( Pt 2): 110-9.
Kabsch, W. and C. Sander (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features." Biopolymers 22(12): 2577-637.
Kunishima, N., Y. Asada, et al. (2005). "A novel induced-fit reaction mechanism of asymmetric hot dog thioesterase PAAI." J Mol Biol 352(1): 212-28.
Li, J., U. Derewenda, et al. (2000). "Crystal structure of the Escherichia coil thioesterase Ⅱ, a homolog of the human Nef binding enzyme." Nat Struct Biol 7(7): 555-9.
Marone, M., S. Mozzetti, et al. (2001). "Semiquantitative RT-PCR analysis to assess the expression levels of multiple transcripts from the same sample." B iol Proced Online 3:19-25.
Meadus, W. J. (2003). "A semi-quantitative RT-PCR method to measure the in vivo effect of dietary conjugated linoleic acid on porcine muscle PPAR gene expression." Biol Proced Online 5: 20-28.
Olivera, E. R., B. Minambres, et al. (1998). "Molecular characterization of the phenylacetic acid catabolic pathway in Pseudomonas putida U: the phenylacetyl-CoA catabolon." Proc Natl Acad Sci U S A 95(11): 6419-24.
Schneider, T. R. and G. M. Sheidrick (2002). "Substructure solution with SHELXD." Acta Crystallogr D Biol Crystallogr 58(Pt 10 Pt 2): 1772-9.
Song, F., Zhuang, Z., Lorenzo Finci, Debra Dunaway-Mariano; Ryan Kniewel, John A. Buglino, Veronica Solorzano, Jin Wu, and Christopher D. Lima. (2006). "Structure, function and mechanism of the phenylacetate pathway hotdog-fold thioesterase Paal." Journal of Biological Chemistry.
Terwilliger, T. C. (1994). "MAD phasing: Bayesian estimates of F(A)." Acta Crystaliogr D Biol Crystallogr 50(Pt 1): 11-6.
Terwilliger, T. C. (2002). "Rapid automatic NCS identification using heavy-atom substructures." Acta Crystallogr D Biol Crystallogr 58(Pt 12): 2213-5.
Vie, M. P., C. Evrard, et al. (1997). "Purification, molecular cloning, and functional expression of the human nicodinamide-adenine dinucleotide phosphate-regulated thyroid hormone-binding protein." Mol Endocrinol 11(11): 1728-36.
Wael Ismail, M. E.-S. M., Barry L. Wanner, Kirill A. Datsenko, Woifgang Eisenreich,Felix Rohdich, Adelbert Bacher and Georg Fuchs (2003). "Functional genomics by NMR spectroscopy Phenylacetate catabolism in Escherichia coli." Eur. J. Biochem 270: 3047-3054.
Abe, S., T. Katagiri, et al. (2003). "Identification of CRYM as a candidate responsible for nonsyndromic deafness, through cDNA microarray analysis of human cochlear and vestibular tissues." Am J Hum Genet 72(1): 73-82.
Apriletti, J. W., J. D. Baxter, et al. (1995). "Expression of the rat alpha 1 thyroid hormone receptor ligand binding domain in Escherichia coli and the use of a ligand-induced conformation change as a method for its purification to homogeneity." Protein Expr Purif 6(3): 363-70.
Baker, P. J., K. L. Britton, et al. (1992). "Structural consequences of sequence patterns in the fingerprint region of the nucleotide binding fold. Implications for nucleotide specificity." J Mol Biol 228(2): 662-71.
Carugo, O. and P. Argos (1997). "NADP-dependent enzymes. I: Conserved stereochemistry of cofactor binding." Proteins 28(1): 10-28.
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