Structural insights into RNA recognition properties of glyceraldehyde-3-phosphate dehydrogenase 3 from Saccharomyces cerevisiae

IUBMB Life

Volumn 66, Issue 9, 2014, Pages 631-638

  Shen, Hui ^a   Wang, Hong ^a   Liu, Qiao ^a   Liu, Huihui ^a   Teng, Maikun ^a   Li, Xu ^a  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

crystal structure; GAPDH3; RNA binding; RNA recognition model; sequence specificity

Indexed keywords

GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE 3; RNA; UNCLASSIFIED DRUG; PROTEIN BINDING;

ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; NONHUMAN; PROTEIN RNA BINDING; RNA RECOGNITION; SACCHAROMYCES CEREVISIAE; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; FLUORESCENCE POLARIZATION; METABOLISM; PROTEIN CONFORMATION;

SACCHAROMYCES CEREVISIAE;

FLUORESCENCE POLARIZATION; GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASES; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; RNA; SACCHAROMYCES CEREVISIAE; SUBSTRATE SPECIFICITY;

EID: 84926021392     PISSN: 15216543     EISSN: 15216551     Source Type: Journal    
DOI: 10.1002/iub.1313     Document Type: Article

References (29)

1. Nicholls, C., Li, H., and, Liu, J. P., (2012) GAPDH: a common enzyme with uncommon functions. Clin. Exp. Pharmacol. Physiol. 39, 674-679.
2. Nagy, E., and, Rigby, W. F. C., (1995) Glyceraldehyde-3-phosphate dehydrogenase selectively binds Au-rich RNA in the Nad(+)-binding region (Rossmann Fold). J. Biol. Chem. 270, 2755-2763.
3. Colell, A., Green, D. R., and, Ricci, J. E., (2009) Novel roles for GAPDH in cell death and carcinogenesis. Cell Death Differ. 16, 1573-1581.
4. Jenkins, J. L., and, Tanner, J. J., (2006) High-resolution structure of human d -glyceraldehyde-3-phosphate dehydrogenase. Acta Crystallogr. D Biol. Crystallogr. 62, 290-301.
5. Sirover, M. A., (1999) New insights into an old protein: the functional diversity of mammalian glyceraldehyde-3-phosphate dehydrogenase. Biochim. Biophys. Acta 1432, 159-184.
6. Zhou, Y., Yi, X., Stoffer, J. B., Bonafe, N., Gilmore-Hebert, M., et al. (2008) The multifunctional protein glyceraldehyde-3-phosphate dehydrogenase is both regulated and controls colony-stimulating factor-1 messenger RNA stability in ovarian cancer. Mol. Cancer Res. 6, 1375-1384.
7. Sirover, M. A., (2012) Subcellular dynamics of multifunctional protein regulation: mechanisms of GAPDH intracellular translocation. J. Cell. Biochem. 113, 2193-2200.
8. Delgado, M. L., O'Connor, J. E., Azorin, I., Renau-Piqueras, J., Gil, M. L., et al. (2001) The glyceraldehyde-3-phosphate dehydrogenase polypeptides encoded by the Saccharomyces cerevisiae TDH1, TDH2 and TDH3 genes are also cell wall proteins. Microbiology 147, 411-417.
9. McAlister, L., and, Holland, M. J., (1985) Isolation and characterization of yeast strains carrying mutations in the glyceraldehyde-3-phosphate dehydrogenase genes. J. Biol. Chem. 260, 15013-15018.
10. Karpel, R. L., and, Burchard, A. C., (1981) A basic isozyme of yeast glyceraldehyde-3-phosphate dehydrogenase with nucleic acid helix-destabilizing activity. Biochim. Biophys. Acta 654, 256-267.
11. Liu, Q., Wang, H., Liu, H., Teng, M., and, Li, X., (2012) Preliminary crystallographic analysis of glyceraldehyde-3-phosphate dehydrogenase 3 from Saccharomyces cerevisiae. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 68, 978-980.
12. Otwinowski, Z., and, Minor, W., (1997) Processing of X-ray diffraction data collected in oscillation mode. Macromol. Crystallogr. A 276, 307-326.
13. Vagin, A., and, Teplyakov, A., (1997) MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 30, 1022-1025.
14. Bailey, S., (1994) The Ccp4 suite-programs for protein crystallography. Acta Crystallogr. D 50, 760-763.
15. Duee, E., Olivier-Deyris, L., Fanchon, E., Corbier, C., Branlant, G., et al. (1996) Comparison of the structures of wild-type and a N313T mutant of Escherichia coli glyceraldehyde 3-phosphate dehydrogenases: implication for NAD binding and cooperativity. J. Mol. Biol. 257, 814-838.
16. 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.
17. Emsley, P., and, Cowtan, K., (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr. Sect. D: Biol. Crystallogr. 60, 2126-2132.
18. Laskowski, R. A., Rullmann, J. A. C., MacArthur, M. W., Kaptein, R., and, Thornton, J. M., (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8, 477-486.
19. Modun, B., and, Williams, P., (1999) The staphylococcal transferrin-binding protein is a cell wall glyceraldehyde-3-phosphate dehydrogenase. Infect. Immun. 67, 1086-1092.
20. Rao, S. T., and, Rossmann, M. G., (1973) Comparison of super-secondary structures in proteins. J. Mol. Biol. 76, 241-256.
21. Mukherjee, S., Dutta, D., Saha, B., and, Das, A. K., (2010) Crystal structure of glyceraldehyde-3-phosphate dehydrogenase 1 from methicillin-resistant Staphylococcus aureus MRSA252 provides novel insights into substrate binding and catalytic mechanism. J. Mol. Biol. 401, 949-968.
22. Engel, M., Seifert, M., Theisinger, B., Seyfert, U., and, Welter, C., (1998) Glyceraldehyde-3-phosphate dehydrogenase and Nm23-H1/nucleoside diphosphate kinase A. Two old enzymes combine for the novel Nm23 protein phosphotransferase function. J. Biol. Chem. 273, 20058-20065.
23. Roitel, O., Sergienko, E., and, Branlant, G., (1999) Dimers generated from tetrameric phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus are inactive but exhibit cooperativity in NAD binding. Biochemistry 38, 16084-16091.
24. Carlile, G. W., Chalmers-Redman, R. M., Tatton, N. A., Pong, A., Borden, K. E., et al. (2000) Reduced apoptosis after nerve growth factor and serum withdrawal: conversion of tetrameric glyceraldehyde-3-phosphate dehydrogenase to a dimer. Mol. Pharmacol. 57, 2-12.
25. Roitel, O., Vachette, P., Azza, S., and, Branlant, G., (2003) P but not R-axis interface is involved in cooperative binding of NAD on tetrameric phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus. J. Mol. Biol. 326, 1513-1522.
26. Corbin, I. R., Gong, Y., Zhang, M., and, Minuk, G. Y., (2002) Proliferative and nutritional dependent regulation of glyceraldehyde-3-phosphate dehydrogenase expression in the rat liver. Cell Prolif. 35, 173-182.
27. Krissinel, E., and, Henrick, K., (2007) Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774-797.
28. Singh, R., and, Green, M. R., (1993) Sequence-specific binding of transfer RNA by glyceraldehyde-3-phosphate dehydrogenase. Science 259, 365-368.
29. Schultz, D. E., Hardin, C. C., and, Lemon, S. M., (1996) Specific interaction of glyceraldehyde 3-phosphate dehydrogenase with the 5?-nontranslated RNA of hepatitis A virus. J. Biol. Chem. 271, 14134-14142.