Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2 ', 5 ')guanosine(538 views) Vitagliano L, Merlino A, Zagari A, Mazzarella L
Protein Sci (ISSN: 0961-8368, 1469-896xelectronic), 2000 Jun; 9(6): 1217-1225.
Keywords: Protein Structure-Function, Protein-Inhibitor Complex, Retro-Binding, Ribonuclease, X-Ray Diffraction, Dinucleotide, Guanosine Derivative, Protein Inhibitor, Article, Binding Affinity, Crystal Structure, Enzyme Active Site, Enzyme Binding, Enzyme Structure, Hydrogen Bond, Priority Journal, Site Directed Mutagenesis, Structure Activity Relation, X Ray Diffraction, Crystallography, Dinucleoside Phosphates, Models, Molecular, Protein Binding, Protein Conformation, Pancreatic, Bryophyta,
Affiliations: Ctro. di Stud. di Biocristallografia, CNR, Univ.' Studi di Napoli Federico II, Via Mezzocannone 4, 1-80134 Napoli, Italy
Dipartimento di Chimica, Univ.' Studi di Napoli Federico II, Via Mezzocannone 4, 1-80134 Napoli, Italy
References: Aguilar, C.F., Thomas, P.J., Mills, A., Moss, D.S., Palmer, R.A., Newly observed binding mode in pancreatic ribonuclease (1992) J Mol Biol, 224, pp. 265-26
Allen, F.H., Bellard, S., Brice, M.D., Cartwright, B.A., Doubleday, A., Higgs, H., Hummelink, T., Motherwell, W.D.S., The Camhridge Crystallographic Data Centre: Computer-based search, retrieval, analysis and display of information (1979) Acta Crystallogr, B35, pp. 2331-2339
Beintema, J.J., Schuller, C., Irie, M., Carsana, A., Molecular evolution of the rihonuclease superfamily (1988) Prog Biophys Mol Biol, 51, pp. 165-192
Benner, S.A., Allemann, R.K., The return of pancreatic ribonucleases (1989) Trends Biochem Sci, 14, pp. 396-397
Berisio, R., Lamzin, V.S., Sica, F., Wilson, K.S., Zagari, A., Mazzarella, L., Protein titration in the crystal state (1999) J Mol Biol, 292, pp. 845-854
Brünger, A.T., (1992) X-PLOR V3.1 User's Guide. A System for X-ray Crystallography and NMR, , New Haven, Connecticut: Yale University Press
Campbell, R.L., Petsko, G.A., Ribonuclease structure and catalysis: Crystal structure of sulfate-free native ribonuclease A at 1.5 Å resolution (1987) Biochemistry, 26, pp. 8579-8584
Chang, C.F., Chen, C., Chen, Y.C., Hom, K., Huang, R.F., Huang, T.H., The solution structure of a cytotoxic ribonuclease from the oocytes of Rana catesbiana (bullfrog) (1998) J Mol Biol, 283, pp. 231-244
Cardayré, S.B., Raines, R.T., A residue to residue hydrogen bond mediates the nucleotide specificity of ribonuclease A (1995) J Mol Biol, 252, pp. 328-336
Cardayré, S.B., Ribo, M., Yokel, E.M., Quirk, D.J., Rutter, W.J., Raines, R.T., Engineering ribonuclease A: Production, purification and characterization of wild-type enzyme and mutants at GlnI 1 (1995) Protein Eng, 8, pp. 261-273
Esnouf, R.M., An extensively modified version of MolScript that includes greatly enhanced coloring capabilities (1997) J Mol Graph, 15, pp. 132-134
Fisher, B.M., Schultz, L.W., Raines, R.T., Coulombic effects of remote subsites on the active site of ribonuclease A (1998) Biochemistry, 37, pp. 17386-17401
Fontecilla-Camps, J.C., De Llorens, R., Du, M.H.L., Cuchillo, C.M., Crystal structure of ribonuclease A d(ApTpApApG) complex (1994) J Biol Chem, 269, pp. 21526-21531
Gilliland, G.L., Crystallographic studies of ribonuclease complexes (1997) Ribonucleases: Structures and Functions, pp. 306-341. , D'Alessio G, Riordan JF, eds. New York: Academic Press
Gilliland, G.L., Dill, J., Pechik, L., Svensson, L.A., Sjölin, L., The active site of bovine pancreatic ribonuclease: An example of solvent modulated specificity (1994) Protein Pept Lett, 1, pp. 60-65
Jones, T.A., Zou, J.-Y., Cowan, S.W., Kjeldgaard, M., Improved methods for building protein models in electron-density maps and the location of errors in these models (1991) Acta Crystallogr, A47, pp. 110-119
Katoh, H., Yoshinaga, M., Yanagita, T., Ohgi, K., Irie, M., Beintema, J.J., Meinsma, D., Kinetic studies on turtle pancreatic ribonuclease: A comparative study of the base specificities of the B2 and P0 sites of bovine pancreatic ribonuclease A and turtle pancreatic ribonuclease (1986) Biochim Biophys Acta, 873, pp. 367-371
Kraulis, P.J., MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures (1991) J Appl Crystallogr, 24, pp. 946-950
Laskowski, R.A., MacArthur, M.W., Moss, D.S., Thornton, J.M., PROCHECK: A program to check the stereochemical quality of protein structure (1993) J Appl Crystallogr, 26, pp. 283-291
Leonidas, D.D., Shapiro, R., Irons, L.I., Russo, N., Acharya, K.R., Crystal structures of ribonuclease A complexes with 5′-diphosphoadenosine 3′-phosphate and 5′-diphosphoadenosine 2′-phosphate at 1.7 Å resolution (1997) Biochemistry, 36, pp. 5578-5588
Lisgarten, J.N., Gupta, V., Maes, D., Wyns, L., Zegers, I., Palmer, R.A., Dealwus, C.G., Hemmings, A.M., Structure of the crystalline complex of cytidylic acid (2′-CMP) with ribonuclease at 1.6 Å resolution. Conservation of solvent site in RNase A at high-resolution structures (1993) Acta Crystallogr, D49, pp. 541-547
Lisgarten, J.N., Maes, D., Wyns, L., Aguilar, C.F., Palmer, R., Structure of the crystalline complex of deoxycytidylyl-3′.5′-guanosine (3′.5′-dCpdG) cocrystallized with ribonuclease at 1.9 Å resolution (1995) Acta Crystallogr, D51, pp. 767-771
Moodie, S.L., Thornton, J.M., A study into the effects of protein binding on nucleotide conformation (1993) Nucleic Acid Res., 21, pp. 1369-1380
Otwinoski, Z., Minor, W., Processing X-ray diffraction data collected in oscillation mode (1997) Methods Enzymol, 276, pp. 307-326
Raines, T.A., Ribonuclease A (1998) Chem Rev, 98, pp. 1045-1066
Richards, F.M., Wyckoff, H.W., Ribonuclease S (1973) Atlas of Molecular Structures in Biology, 1. , Philips DC, Richards FM, eds. Oxford, UK: Claderon
Schultz, L.W., Quirk, D.J., Raines, R.T., His ⋯ Asp catalytic dyad of ribonuclease A: Structure and function of the wild-type. D12IN, and D12IA enzymes (1998) Biochemistry, 37, pp. 8886-8898
Tarragona-Fiol, A., Eggelte, H.J., Harbron, S., Sanchcez, E., Taylorson, C.J., Ward, J.M., Rabin, B.R., Identification by site-directed mutagenesis of amino acids in the B2 subsite of bovine pancreatic ribonuclease A (1993) Protein Eng, 6, pp. 901-906
Toiron, C., Gonzalez, C., Bruix, M., Rico, M., Three-dimensional structure of the complex of ribonuclcase A with 2′.5′-CpA and 3′.5′-d(CpA) in aqueous solution, as obtained by NMR and restrained molecular dynamics (1996) Protein Sci, 5, pp. 1633-1647
Usher, D.A., On the mechanism of ribonuclease action (1969) Proc Natl Acad Sci USA, 62, pp. 661-667
Vitugliano, L., Adinolfi, S., Riccio, A., Sica, F., Zagari, A., Mazzarella, L., Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl (2′-5′)adenosine (1998) Protein Sci, 7, pp. 1691-11644
Vitagliano, L., Adinolfi, S., Sica, F., Merlino, A., Zagari, A., Mazzarella, L., A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease (1999) J Mol Biol, 293, pp. 566-577
Wladkwosky, B.D., Svensson, L.A., Sjölin, L., Ladner, J.E., Gilliland, G.L., Structure (1.3 Å) and charge state of a ribonuclease A-vanadate complex: Implications for the phosphate ester hydrolysis mechanism (1998) J Am Chem Soc, 120, pp. 5488-5498
Wlodawer, A., Miller, M., Sjölin, L., Active site of RNase: Neutron diffraction study of a complex with uridine vanadate, a transition-state analogue (1983) Proc Natl Acad Sci USA, 80, pp. 3628-3631
Wlodawer, A., Sjölin, L., Application of joint neutron and X-ray refinement to the investigation of the structure of ribonuclease A at 2.0 Å resolution (1983) Biochemistry, 22, pp. 2720-2728
Wlodawer, A., Svensson, L.A., Sjölin, L., Gilliland, G.L., Structure of phosphate-free ribonuclease A refined at 1.26 Å (1988) Biochemistry, 27, pp. 2705-2717
Wodak, S.Y., Liu, M.Y., Wyckoff, H.W., The structure of cytidilyl (2′,5′) adenosine when bound to pancreatic ribonuclease S (1977) J Mol Biol, 116, pp. 855-875
Youle, R.J., D'Alessio, G., Antitumor RNases (1997) Ribonucleases: Structures and Functions, pp. 491-514. , D'Alessio G, Riordan JF, eds. New York: Academic Press
Zegers, I., Maes, D., Dao-Thi, M.-H., Poortmans, F., Palmer, R., Wyns, L., The structures of RNase A complexed with 3′-CMP and d(CpA): Active site conformation and conserved water molecules (1994) Protein Sci, 3, pp. 2322-2339
Aguilar, C. F., Thomas, P. J., Mills, A., Moss, D. S., Palmer, R. A., Newly observed binding mode in pancreatic ribonuclease (1992) J Mol Biol, 224, pp. 265-26
Allen, F. H., Bellard, S., Brice, M. D., Cartwright, B. A., Doubleday, A., Higgs, H., Hummelink, T., Motherwell, W. D. S., The Camhridge Crystallographic Data Centre: Computer-based search, retrieval, analysis and display of information (1979) Acta Crystallogr, B35, pp. 2331-2339
Beintema, J. J., Schuller, C., Irie, M., Carsana, A., Molecular evolution of the rihonuclease superfamily (1988) Prog Biophys Mol Biol, 51, pp. 165-192
Benner, S. A., Allemann, R. K., The return of pancreatic ribonucleases (1989) Trends Biochem Sci, 14, pp. 396-397
Br nger, A. T., (1992) X-PLOR V3. 1 User's Guide. A System for X-ray Crystallography and NMR, , New Haven, Connecticut: Yale University Press
Campbell, R. L., Petsko, G. A., Ribonuclease structure and catalysis: Crystal structure of sulfate-free native ribonuclease A at 1. 5 resolution (1987) Biochemistry, 26, pp. 8579-8584
Chang, C. F., Chen, C., Chen, Y. C., Hom, K., Huang, R. F., Huang, T. H., The solution structure of a cytotoxic ribonuclease from the oocytes of Rana catesbiana (bullfrog) (1998) J Mol Biol, 283, pp. 231-244
Cardayr, S. B., Raines, R. T., A residue to residue hydrogen bond mediates the nucleotide specificity of ribonuclease A (1995) J Mol Biol, 252, pp. 328-336
Cardayr, S. B., Ribo, M., Yokel, E. M., Quirk, D. J., Rutter, W. J., Raines, R. T., Engineering ribonuclease A: Production, purification and characterization of wild-type enzyme and mutants at GlnI 1 (1995) Protein Eng, 8, pp. 261-273
Esnouf, R. M., An extensively modified version of MolScript that includes greatly enhanced coloring capabilities (1997) J Mol Graph, 15, pp. 132-134
Fisher, B. M., Schultz, L. W., Raines, R. T., Coulombic effects of remote subsites on the active site of ribonuclease A (1998) Biochemistry, 37, pp. 17386-17401
Gilliland, G. L., Crystallographic studies of ribonuclease complexes (1997) Ribonucleases: Structures and Functions, pp. 306-341. , D'Alessio G, Riordan JF, eds. New York: Academic Press
Gilliland, G. L., Dill, J., Pechik, L., Svensson, L. A., Sj lin, L., The active site of bovine pancreatic ribonuclease: An example of solvent modulated specificity (1994) Protein Pept Lett, 1, pp. 60-65
Jones, T. A., Zou, J. -Y., Cowan, S. W., Kjeldgaard, M., Improved methods for building protein models in electron-density maps and the location of errors in these models (1991) Acta Crystallogr, A47, pp. 110-119
Kraulis, P. J., MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures (1991) J Appl Crystallogr, 24, pp. 946-950
Laskowski, R. A., MacArthur, M. W., Moss, D. S., Thornton, J. M., PROCHECK: A program to check the stereochemical quality of protein structure (1993) J Appl Crystallogr, 26, pp. 283-291
Leonidas, D. D., Shapiro, R., Irons, L. I., Russo, N., Acharya, K. R., Crystal structures of ribonuclease A complexes with 5 -diphosphoadenosine 3 -phosphate and 5 -diphosphoadenosine 2 -phosphate at 1. 7 resolution (1997) Biochemistry, 36, pp. 5578-5588
Lisgarten, J. N., Gupta, V., Maes, D., Wyns, L., Zegers, I., Palmer, R. A., Dealwus, C. G., Hemmings, A. M., Structure of the crystalline complex of cytidylic acid (2 -CMP) with ribonuclease at 1. 6 resolution. Conservation of solvent site in RNase A at high-resolution structures (1993) Acta Crystallogr, D49, pp. 541-547
Lisgarten, J. N., Maes, D., Wyns, L., Aguilar, C. F., Palmer, R., Structure of the crystalline complex of deoxycytidylyl-3. 5 -guanosine (3. 5 -dCpdG) cocrystallized with ribonuclease at 1. 9 resolution (1995) Acta Crystallogr, D51, pp. 767-771
Moodie, S. L., Thornton, J. M., A study into the effects of protein binding on nucleotide conformation (1993) Nucleic Acid Res., 21, pp. 1369-1380
Raines, T. A., Ribonuclease A (1998) Chem Rev, 98, pp. 1045-1066
Richards, F. M., Wyckoff, H. W., Ribonuclease S (1973) Atlas of Molecular Structures in Biology, 1. , Philips DC, Richards FM, eds. Oxford, UK: Claderon
Schultz, L. W., Quirk, D. J., Raines, R. T., His Asp catalytic dyad of ribonuclease A: Structure and function of the wild-type. D12IN, and D12IA enzymes (1998) Biochemistry, 37, pp. 8886-8898
Usher, D. A., On the mechanism of ribonuclease action (1969) Proc Natl Acad Sci USA, 62, pp. 661-667
Wladkwosky, B. D., Svensson, L. A., Sj lin, L., Ladner, J. E., Gilliland, G. L., Structure (1. 3) and charge state of a ribonuclease A-vanadate complex: Implications for the phosphate ester hydrolysis mechanism (1998) J Am Chem Soc, 120, pp. 5488-5498
Wlodawer, A., Sj lin, L., Application of joint neutron and X-ray refinement to the investigation of the structure of ribonuclease A at 2. 0 resolution (1983) Biochemistry, 22, pp. 2720-2728
Wodak, S. Y., Liu, M. Y., Wyckoff, H. W., The structure of cytidilyl (2, 5) adenosine when bound to pancreatic ribonuclease S (1977) J Mol Biol, 116, pp. 855-875
Youle, R. J., D'Alessio, G., Antitumor RNases (1997) Ribonucleases: Structures and Functions, pp. 491-514. , D'Alessio G, Riordan JF, eds. New York: Academic Press
Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2 ', 5 ')guanosine
Guanine-containing mono- and dinucleotides bind to the active site of ribonuclease A in a nonproductive mode (retro-binding) (Aguilar CF, Thomas PJ, Mills A, Moss DS, Palmer RA, 1992, J Mol Biol 224:265-267). Guanine binds to the highly specific pyrimidine site by forming hydrogen bonds with Thr45 and with the sulfate anion located in the P1 site, To investigate the influence of the anion present in the P1 site on retro-binding, we determined the structure of two new complexes of RNase A with uridylyl(2',5')guanosine obtained by soaking two different forms of pre-grown RNase A crystals. In one case, RNase A was crystallized without removing the sulfate anion strongly bound to the active site; in the other, the protein was first equilibrated with a basic solution to displace the anion from the Pi site. The X-ray structures of the complexes with and without sulfate in P1 were refined using diffraction data up to 1.8 Angstrom (R-factor 0.192) and 2.0 Angstrom (R-factor 0.178), respectively The binding mode of the substrate analogue to the protein differs markedly in the two complexes. When the sulfate is located in P1, we observe retro-binding; whereas when the anion is removed from the active site, the uridine is productively bound at the B1 site. In the productive complex, the electron density is very well defined for the uridine moiety, whereas the downstream guanine is disordered. This finding indicates that the interactions of guanine in the B2 site are rather weak and that this site is essentially adenine preferring. In this crystal farm. there are two molecules per asymmetric unit. and due to crystal packing, only the active site of one molecule is accessible to the ligand. Thus, in the same crystal we have a ligand-bound and a ligand-free RNase A molecule. The comparison of these two structures furnishes a detailed and reliable picture of the structural alterations induced by the binding of the substrate. These results provide structural information to support the hypotheses on the role of RNase A active site residues that have recently emerged from site-directed mutagenesis studies.
Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2 ', 5 ')guanosine
No results.
Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2 ', 5 ')guanosine