The solution structure of apo-iron regulatory protein 1

Gene

Volumn 524, Issue 2, 2013, Pages 341-346

  Shand, O'Neil ^a   Volz, Karl ^a  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

Bifunctionality; Iron homeostasis; Iron regulatory protein; Iron sulfur cluster; RNA binding

Indexed keywords

IRON REGULATORY PROTEIN 1; MESSENGER RNA; SULFUR;

AB INITIO CALCULATION; ARTICLE; IRON RESPONSIVE ELEMENT; PRIORITY JOURNAL; PROTEIN STRUCTURE; RNA BINDING; X RAY CRYSTALLOGRAPHY;

ANIMALS; APOLIPOPROTEINS; CRYSTALLOGRAPHY, X-RAY; CYTOSOL; IRON REGULATORY PROTEIN 1; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; RABBITS; RNA; RNA-BINDING PROTEINS; SACCHAROMYCES CEREVISIAE; SCATTERING, SMALL ANGLE; SOLUTIONS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84878625223     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2013.03.112     Document Type: Article

References (41)

1. Alén C., Sonenshein A.L. Bacillus subtilis aconitase is an RNA-binding protein. Proc. Natl. Acad. Sci. U. S. A. 2002, 96:10412-10417.
2. Anderson C.P., Shen M., Eisenstein R.S., Leibold E.A. Mammalian iron metabolism and its control by iron regulatory proteins. Biochim. Biophys. Acta 2012, 1823:1468-1483.
3. Arnaud N., et al. The iron-responsive element (IRE)/iron-regulatory protein 1 (IRP1)-cytosolic aconitase iron-regulatory switch does not operate in plants. Biochem. J. 2007, 405:523-531.
4. Baughn A.D., Malamy M.H. A mitochondrial-like aconitase in the bacterium Bacteroides fragilis: implications for the evolution of the mitochondrial Krebs cycle. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:4662-4667.
5. Beinert H., Kennedy M.C. Aconitase: a two-faced protein: enzyme and iron-regulatory factor. FASEB J. 1993, 7:1442-1449.
6. Bernadó P. Effects of interdomain dynamics on the structure determination of modular proteins by small-angle scattering. Eur. Biophys. J. 2010, 39:769-780.
7. Bernadó P., Mylonas E., Petoukhov M.V., Blackledge M., Svergun D.I. Structural characterization of flexible proteins using small-angle X-ray scattering. J. Am. Chem. Soc. 2007, 129:5656-5664.
8. Brazzolotto X., Timmins P., Dupont Y., Moulis J.-M. Structural changes associated with switching activities of human iron regulatory protein 1. J. Biol. Chem. 2002, 277:11995-12000.
9. DeLano W.L. The PyMOL Molecular Graphics System 2002, DeLano Scientific, San Carlos, CA.
10. Dong H., Qin S., Zhou H.-X. Effects of macromolecular crowding on protein conformational changes. PLoS Comput. Biol. 2010, 6:e1000833.
11. Dupuy J., Volbeda A., Carpentier P., Darnault C., Moulis J.-M., Fontecilla-Camps J.C. Crystal structure of human iron regulatory protein 1 as c-aconitase. Structure 2006, 14:129-139.
12. Fischer H., de Oliveira Neto M., Napolitano H.B., Polikarpov I., Craievich A.F. Determination of the molecular weight of proteins in solution from a single small-angle X-ray scattering measurement on a relative scale. J. Appl. Cryst. 2010, 43:101-109.
13. Fischetti R., et al. The BioCAT undulator beamline 18ID: a facility for biological non-crystalline diffraction and X-ray absorption spectroscopy at the advanced photon source. J. Synchrotron Radiat. 2004, 11:399-405.
14. Gasteiger E., et al. Protein identification and analysis tools on the ExPASy server. The Proteomics Protols Handbook 2005, 571-607.
15. Gruer M.J., Artymiuk P.J., Guest J.R. The aconitase family: three structural variations on a common theme. Trends Biochem. Sci. 1997, 22:3-6.
16. Kilburn D., Roh J.H., Guo L., Briber R.M., Woodson S.A. Molecular crowding stabilizes folded RNA structure by the excluded volume effect. J. Am. Chem. Soc. 2010, 132:8690-8696.
17. Kozin M.B., Svergun D.I. Automated matching of high- and low-resolution structural models. J. Appl. Crystallogr. 2001, 34:33-41.
18. Lauble H., Stout C.D. Steric and conformational features of the aconitase mechanism. Proteins 1995, 22:1-11.
19. Makarova K.S., Koonin E.V. Filling a gap in the central metabolism of archaea: prediction of a novel aconitase by comparative-genomic analysis. FEMS Microbiol. Lett. 2003, 27:17-23.
20. 2 biogenesis and transfer. Angew. Chem. Int. Ed. 2012, 51:5439-5442.
21. McCallum S.A., Pardi A. Refined solution structure of the iron-responsive element RNA using residual dipolar couplings. J. Mol. Biol. 2003, 326:1037-1050.
22. Petoukhov M.V., Svergun D.I. Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophys. J. 2005, 89:1237-1250.
23. Piccinelli P., Samuelsson T. Evolution of the iron-responsive element. RNA 2007, 13:952-966.
24. Schalinske K.L., Anderson S.A., Tuazon P.T., Chen O.S., Kennedy M.C., Eisenstein R.S. The iron-sulfur cluster of iron regulatory protein 1 modulates the accessibility of RNA binding and phosphorylation sites. Biochemistry 1997, 36:3950-3958.
25. Selezneva A.I., Cavigiolio G., Theil E.C., Walden W.E., Volz K. Crystallization and preliminary X-ray diffraction analysis of iron regulatory protein-1 in complex with ferritin IRE RNA. Acta Crystallogr. 2006, F62:249-252.
26. Sharma A.K., Pallesen L.J., Spang R.J., Walden W.E. Cytosolic iron-sulfur cluster assembly (CIA) system: factors, mechanism, and relevance to cellular iron regulation. J. Biol. Chem. 2010, 285:26745-26751.
27. Shi R., et al. Structural basis for Fe-S cluster assembly and tRNA thiolation mediated by IscS protein-protein interactions. PLoS Biol. 2010, 8:e1000354.
28. Showalter S.A., Baker N.A., Tang C., Hall K.B. Iron responsive element RNA flexibility described by NMR and isotropic reorientational eigenmode dynamics. J. Biomol. NMR 2005, 32:179-193.
29. Svergun D.I., Barberato C., Koch M.H.J. CRYSOL: a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Cryst. 1995, 28:768-773.
30. Svergun D.I., Petoukhov M.V., Koch M.H.J. Determination of domain structure of proteins from X-ray solution scattering. Biophys. J. 2001, 80:2946-2953.
31. Swenson G.R., Walden W.E. Localization of an RNA binding element of the iron responsive element binding protein within a proteolytic fragment containing iron coordination ligands. Nucleic Acids Res. 1994, 22:2627-2633.
32. Tang Y., Guest J.R. Direct evidence for mRNA binding and post-transcriptional regulation by Escherichia coli aconitases. Microbiology 1999, 145:3069-3079.
33. Tang Y., Guest J.R., Artymiuk P.J., Green J. Switching aconitase B between catalytic and regulatory modes involves iron-dependent dimer formation. Mol. Microbiol. 2005, 56:1149-1158.
34. Tsuchiya D., Shimizu N., Tomita M. Versatile architecture of a bacterial aconitase B and its catalytic performance in the sequential reaction coupled with isocitrate dehydrogenase. Biochim. Biophys. Acta 2008, 1784:1847-1856.
35. Tsuchiya D., Shimizu N., Tomita M. Cooperativity of two active sites in bacterial homodimeric aconitases. Biochim. Biophys. Res. Comm. 2009, 379:485-488.
36. Volkov V.V., Svergun D.I. Uniqueness of ab initio shape determination in small-angle scattering. J. Appl. Crystallogr. 2003, 36:860-864.
37. Walden W.E., et al. Structure of dual function iron regulatory protein 1 complexed with ferritin IRE-RNA. Science 2006, 314:1903-1909.
38. Walden W.E., Selezneva A., Volz K. Accommodating variety in iron responsive elements: crystal structure of transferrin receptor 1 B IRE bound to iron regulatory protein 1. FEBS Lett. 2012, 586:32-35.
39. Wriggers W., Chacón P. Using Situs for the registration of protein structures with low-resolution bead models from X-ray solution scattering. J. Appl. Crystallogr. 2001, 34:773-776.
40. Yikilmaz E., Rouault T.A., Schuck P. Self-association and ligand-induced conformational changes of iron regulatory proteins 1 and 2. Biochemistry 2005, 44:8470-8478.
41. Zhou H.-X., Rivas G.N., Minton A.P. Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu. Rev. Biophys. 2008, 37:375-397.