Structure Basis for the Regulation of Glyceraldehyde-3-Phosphate Dehydrogenase Activity via the Intrinsically Disordered Protein CP12

Structure - Tập 19 - Trang 1846-1854 - 2011
Hiroyoshi Matsumura1,2, Akihiro Kai1, Takayuki Maeda1, Masahiro Tamoi3, Atsuko Satoh1, Haruka Tamura1, Mika Hirose1, Taketo Ogawa, Natsuko Kizu1, Akira Wadano4, Tsuyoshi Inoue1,2, Shigeru Shigeoka3
1Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
2SOSHO, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
3Department of Advanced Bioscience, Faculty of Agriculture, Kinki University, Nakamachi, Nara 631-8505, Japan
4Department of Human Life Science, Hagoromo University of International Study, Sakai, Osaka 592-8344, Japan

Tài liệu tham khảo

Adams, 1997, Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement, Proc. Natl. Acad. Sci. USA, 94, 5018, 10.1073/pnas.94.10.5018 Adams, 2010, PHENIX: a comprehensive Python-based system for macromolecular structure solution, Acta Crystallogr. D Biol. Crystallogr., 66, 213, 10.1107/S0907444909052925 Avilan, 1997, Information transfer in multienzyme complexes—2. The role of Arg64 of Chlamydomonas reinhardtii phosphoribulokinase in the information transfer between glyceraldehyde-3-phosphate dehydrogenase and phosphoribulokinase, Eur. J. Biochem., 250, 296, 10.1111/j.1432-1033.1997.0296a.x Boggetto, 2007, Regulation of phosphoribulokinase and glyceraldehyde 3-phosphate dehydrogenase in a freshwater diatom, Asterionella formosa, J. Phycol., 43, 1227, 10.1111/j.1529-8817.2007.00409.x Buchanan, 1980, Role of light in the regulation of chloroplast enzymes, Annu. Rev. Plant Physiol., 31, 341, 10.1146/annurev.pp.31.060180.002013 Buchanan, 2005, Redox regulation: a broadening horizon, Annu. Rev. Plant Biol., 56, 187, 10.1146/annurev.arplant.56.032604.144246 Delobel, 2005, Mass spectrometric analysis of the interactions between CP12, a chloroplast protein, and metal ions: a possible regulatory role within a PRK/GAPDH/CP12 complex, Rapid Commun. Mass Spectrom., 19, 3379, 10.1002/rcm.2192 Didierjean, 2003, Crystal structure of two ternary complexes of phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus with NAD and D-glyceraldehyde 3-phosphate, J. Biol. Chem., 278, 12968, 10.1074/jbc.M211040200 Dyson, 2002, Coupling of folding and binding for unstructured proteins, Curr. Opin. Struct. Biol., 12, 54, 10.1016/S0959-440X(02)00289-0 Dyson, 2005, Intrinsically unstructured proteins and their functions, Nat. Rev. Mol. Cell Biol., 6, 197, 10.1038/nrm1589 Emsley, 2004, Coot: model-building tools for molecular graphics, Acta Crystallogr. D Biol. Crystallogr., 60, 2126, 10.1107/S0907444904019158 Erales, 2009, CP12 from Chlamydomonas reinhardtii, a permanent specific “chaperone-like” protein of glyceraldehyde-3-phosphate dehydrogenase, J. Biol. Chem., 284, 12735, 10.1074/jbc.M808254200 Erales, 2008, Specificity and function of glyceraldehyde 3-phosphate dehydrogenase in a freshwater diatom, Asterionella formosa (Bacillariophyceae), J. Phycol., 44, 1455, 10.1111/j.1529-8817.2008.00600.x Erales, 2009, Mapping of a copper-binding site on the small CP12 chloroplastic protein of Chlamydomonas reinhardtii using top-down mass spectrometry and site-directed mutagenesis, Biochem. J., 419, 75, 10.1042/BJ20082004 Erales, 2011, Molecular mechanism of NADPH-glyceraldehyde-3-phosphate dehydrogenase regulation through the C-terminus of CP12 in Chlamydomonas reinhardtii, Biochemistry, 50, 2881, 10.1021/bi1020259 Fermani, 2007, Molecular mechanism of thioredoxin regulation in photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase, Proc. Natl. Acad. Sci. USA, 104, 11109, 10.1073/pnas.0611636104 Gardebien, 2006, Construction of a 3D model of CP12, a protein linker, J. Mol. Graph. Model., 25, 186, 10.1016/j.jmgm.2005.12.003 Gouet, 1999, ESPript: analysis of multiple sequence alignments in PostScript, Bioinformatics, 15, 305, 10.1093/bioinformatics/15.4.305 Graciet, 2003, Characterization of native and recombinant A4 glyceraldehyde 3-phosphate dehydrogenase. Kinetic evidence for conformation changes upon association with the small protein CP12, Eur. J. Biochem., 270, 129, 10.1046/j.1432-1033.2003.03372.x Graciet, 2003, The small protein CP12: a protein linker for supramolecular complex assembly, Biochemistry, 42, 8163, 10.1021/bi034474x Heineke, 1991, Redox transfer across the inner chloroplast envelope membrane, Plant Physiol., 95, 1131, 10.1104/pp.95.4.1131 Howard, 2008, Thioredoxin-mediated reversible dissociation of a stromal multiprotein complex in response to changes in light availability, Proc. Natl. Acad. Sci. USA, 105, 4056, 10.1073/pnas.0710518105 Kitatani, 2006, Structure of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Synechococcus PCC7942 complexed with NADP, Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun., 62, 315, 10.1107/S1744309106007378 Kraulis, 1991, MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures, J. Appl. Crystallogr., 24, 946, 10.1107/S0021889891004399 Külheim, 2002, Rapid regulation of light harvesting and plant fitness in the field, Science, 297, 91, 10.1126/science.1072359 Laskowski, 1993, PROCHECK: a program to check the stereochemical quality of protein structures, J. Appl. Crystallogr., 26, 283, 10.1107/S0021889892009944 Lebreton, 2006, Mapping of the interaction site of CP12 with glyceraldehyde-3-phosphate dehydrogenase from Chlamydomonas reinhardtii. Functional consequences for glyceraldehyde-3-phosphate dehydrogenase, FEBS J., 273, 3358, 10.1111/j.1742-4658.2006.05342.x Marri, 2005, Reconstitution and properties of the recombinant glyceraldehyde-3-phosphate dehydrogenase/CP12/phosphoribulokinase supramolecular complex of Arabidopsis, Plant Physiol., 139, 1433, 10.1104/pp.105.068445 Marri, 2008, Spontaneous assembly of photosynthetic supramolecular complexes as mediated by the intrinsically unstructured protein CP12, J. Biol. Chem., 283, 1831, 10.1074/jbc.M705650200 Merritt, 1994, Raster3D Version 2.0. A program for photorealistic molecular graphics, Acta Crystallogr. D Biol. Crystallogr., 50, 869, 10.1107/S0907444994006396 Namba, 2001, Roles of partly unfolded conformations in macromolecular self-assembly, Genes Cells, 6, 1, 10.1046/j.1365-2443.2001.00384.x Nicholls, 1991, Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons, Proteins, 11, 281, 10.1002/prot.340110407 Otwinowski, Z. (1993). Oscillation data reduction program. L. Sawyer, N. Isaacs, and S. Bailey, eds. Proceedings of the CCP4 Study Weekend: Data Collection and Processing. Warrington: Daresbury Laboratory. pp 56–62. Pohlmeyer, 1996, CP12: a small nuclear-encoded chloroplast protein provides novel insights into higher-plant GAPDH evolution, Plant Mol. Biol., 32, 969, 10.1007/BF00020493 Scheibe, 2002, Co-existence of two regulatory NADP-glyceraldehyde 3-P dehydrogenase complexes in higher plant chloroplasts, Eur. J. Biochem., 269, 5617, 10.1046/j.1432-1033.2002.03269.x Tamoi, 1996, Enzymic and molecular characterization of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Synechococcus PCC 7942: resistance of the enzyme to hydrogen peroxide, Biochem. J., 316, 685, 10.1042/bj3160685 Tamoi, 2005, The Calvin cycle in cyanobacteria is regulated by CP12 via the NAD(H)/NADP(H) ratio under light/dark conditions, Plant J., 42, 504, 10.1111/j.1365-313X.2005.02391.x Tompa, 2002, Intrinsically unstructured proteins, Trends Biochem. Sci., 27, 527, 10.1016/S0968-0004(02)02169-2 Trost, 2006, Thioredoxin-dependent regulation of photosynthetic glyceraldehyde-3-phosphate dehydrogenase: autonomous vs. CP12-dependent mechanisms, Photosynth. Res., 89, 263, 10.1007/s11120-006-9099-z Uversky, 2005, Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling, J. Mol. Recognit., 18, 343, 10.1002/jmr.747 Vagin, 1997, MOLREP: an automated program for molecular replacement, J. Appl. Crystallogr., 30, 1022, 10.1107/S0021889897006766 Wallace, 1995, LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions, Protein Eng., 8, 127, 10.1093/protein/8.2.127 Wedel, 1998, Evolutionary conserved light regulation of Calvin cycle activity by NADPH-mediated reversible phosphoribulokinase/CP12/glyceraldehyde-3-phosphate dehydrogenase complex dissociation, Proc. Natl. Acad. Sci. USA, 95, 9699, 10.1073/pnas.95.16.9699 Wedel, 1997, CP12 provides a new mode of light regulation of Calvin cycle activity in higher plants, Proc. Natl. Acad. Sci. USA, 94, 10479, 10.1073/pnas.94.19.10479 Wright, 1999, Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm, J. Mol. Biol., 293, 321, 10.1006/jmbi.1999.3110