Structural studies of the Enterococcus faecalis SufU [Fe-S] cluster protein

BMC Biochemistry

Volumn 10, Issue 1, 2009, Pages

  Riboldi, Gustavo P ^a   Verli, Hugo ^a   Frazzon, Jeverson ^a  

^a FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; ASPARTIC ACID; CYSTEINE; IRON SULFUR PROTEIN; SCAFFOLD PROTEIN; BACTERIAL PROTEIN;

ARTICLE; BACTERIAL GENOME; CARBOXY TERMINAL SEQUENCE; ENTEROCOCCUS FAECALIS; FIRMICUTES; HAEMOPHILUS INFLUENZAE; MOLECULAR DYNAMICS; MOLECULAR MODEL; PHYLOGENY; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; STREPTOCOCCUS PYOGENES; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; GENETICS; GRAM POSITIVE BACTERIUM; METABOLISM; MOLECULAR GENETICS; PROTEIN DATABASE; SEQUENCE HOMOLOGY;

ENTEROCOCCUS; ENTEROCOCCUS FAECALIS; ESCHERICHIA COLI; FIRMICUTES; HAEMOPHILUS INFLUENZAE; NEGIBACTERIA; POSIBACTERIA; STREPTOCOCCUS PYOGENES;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; DATABASES, PROTEIN; ENTEROCOCCUS FAECALIS; GENOME, BACTERIAL; GRAM-POSITIVE BACTERIA; IRON-SULFUR PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN STRUCTURE, SECONDARY; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 60649117402     PISSN: None     EISSN: 14712091     Source Type: Journal    
DOI: 10.1186/1471-2091-10-3     Document Type: Article

References (46)

1. Biosynthesis of iron-sulphur clusters is a complex and highly conserved process. J Frazzon JR Fick DR Dean, Biochem Soc Trans 2002 30 4 680 685 10.1042/BST0300680 12196163
2. Formation of iron-sulfur clusters in bacteria: an emerging field in bioinorganic chemistry. J Frazzon DR Dean, Curr Opinion Cheml Biol 2003 7 166 173 10.1016/S1367-5931(03)00021-8
3. Structure, Function and Formation of Biological Iron-Sulfur Clusters. DC Johnson DR Dean AD Smith MK Johnson, Annu Rev Biochem 2005 74 247 81 10.1146/annurev.biochem.74.082803.133518 15952888
4. Maturation of Iron-Sulfur Proteins in Eukaryotes: Mechanisms, Connected Processes, and Diseases. R Lill U Mühlenhoff, Annu Rev Biochem 2008 77 669 700 10.1146/annurev.biochem.76.052705.162653 18366324
5. The reconstitution of Clostridial ferredoxin. R Malkin JC Rabinowitz, Biochem Biophys Res Comm 1966 23 822 827 10.1016/0006-291X(66)90561-4 5962494
6. RP Hausinger GL Eichorn LG Marzilli Eds, Mechanisms of Metallocenter Assembly New York: Wiley 1996
7. Fe-S proteins in sensing and regulatory functions. H Beinert PJ Kiley, Curr Opin Chem Biol 1999 3 2 152 7 10.1016/S1367-5931(99)80027-1 10226040
8. Iron-sulfur proteins: ancient structures, still full of surprises. H Beinert, J Biol Inorg Chem 2000 5 1 2 15 10.1007/s007750050002 10766431
9. The role of Fe-S proteins in sensing and regulation in bacteria. PJ Kiley H Beinert, Curr Opin Microbiol 2003 6 2 181 5 10.1016/S1369-5274(03)00039-0 12732309
10. Physical and Genetic Map of the Major nif Gene Cluster from Azotobacter vinelandii. MR Jacobson KE Brigle L Bennett RA Setterquist MS Wilson VL Cash J Beynon WE Newton D Dean, J Bacteriol 1989 171 2 1017 1027 2644218
11. Biochemical and genetic analysis of the nifUSVWZM cluster from Azotobacter vinelandii. MR Jacobson VL Cash MC Weiss NF Laird WE Newton DR Dean, Mol Gen Genet 1989 219 49 57 10.1007/BF00261156 2615765
12. Assembly of iron sulfur clusters: identification of an iscSUA-hscBA-fdx gene cluster from Azotobacter vinelandii. L Zheng VL Cash DH Flint DR Dean, J Biol Chem 1998 273 13264 13272 10.1074/jbc.273.21.13264 9582371
13. Mechanisms of iron-sulfur cluster assembly: the SUF machinery. M Fontecave S Ollagnier de Choudens F Barras, J Biol Inorg Chem 2005 10 713 721 10.1007/s00775-005-0025-1 16211402
14. A third bacterial system for the assembly of iron-sulfur clusters with homologs in archea and plastids. Y Takahashi U Tokumoto, J Biol Chem 2002 277 28380 28383 10.1074/jbc.C200365200 12089140
15. Iron-Sulfur Cluster Biosynthesis: Toward an Understanding of Cellular Machinery and Molecular Mechanism. S Mansy JA Cowan, Acc Chem Res 2004 37 719 725 10.1021/ar0301781 15379587
16. IscU as a Scaffold for Iron-Sulfur Cluster Biosynthesis: Sequential Assembly of [2Fe-2S] and [4Fe-4S] Clusters in IscU. JN Agar C Krebs J Frazzon BH Huynh DR Dean MK Johnson, Biochemistry 2000 39 7856 7862 10.1021/bi000931n 10891064
17. In vivo iron-sulfur cluster formation. EC Raulfs IP O'Carroll PC Dos Santos MC Unciuleac DR Dean, Proc Natl Acad Sci USA 2008 105 25 8591 8596 18562278 10.1073/pnas.0803173105
18. Cysteine desulfurase activity indicates a role for NIFS in metallocluster biosynthesis. L Zheng RH White VL Cash RF Jack DR Dean, Proc Natl Acad Sci USA 1993 90 2754 2758 8464885 10.1073/pnas.90.7.2754
19. Identification of the Mycobacterium tuberculosis SUF machinery as the exclusive mycobacterial system of [Fe-S] cluster assembly: evidence for its implication in the pathogen's survival. G Huet M Daffé I Saves, J Bacteriol 2005 187 17 6137 6146 16109955 10.1128/JB.187.17.6137-6146.2005
20. SufC: an unorthodox cytoplasmic ABC/ATPase required for [Fe-S] biogenesis under oxidative stress. L Nachin L Loiseau D Expert F Barras, EMBO J 2003 22 427 437 12554644 10.1093/emboj/cdg061
21. Pathogenic enterococci: new developments in the 21st century. PM Tendolkar AS Baghdayan N Shankar, Cell Mol Life Sci 2003 60 2622 2636 10.1007/s00018-003-3138-0 14685687
22. Crystal Structure of IscA, an Iron-sulfur Cluster Assembly Protein from Escherichia coli. JR Cupp-Vickery JJ Silberg T Dennis LE Vickery, J Mol Biol 2004 338 127 137 10.1016/j.jmb.2004.02.027 15050828
23. Crystal structure of Escherichia coli SufA involved in biosynthesis of iron-sulfur clusters: implications for a functional dimer. K Wada Y Hasegawa Z Gong Y Minami K Fukuyama Y Takahashi, FEBS Lett 2005 579 29 6543 6548 10.1016/j.febslet.2005.10.046 16298366
24. Structural Characterization of an Iron-Sulfur Cluster Assembly Protein IscU in a Zinc-Bound Form. J Liu N Oganesyan DH Shin J Jancarik H Yokota R Kim SH Kim, Proteins 2005 59 875 881 10.1002/prot.20421 15815978
25. Solution NMR Structure of the Iron-Sulfur Cluster Assembly Protein U (IscU) with Zinc Bound at the Active Site. TA Ramelot JR Cort S Goldsmith-Fischman GJ Kornhaber R Xiao R Shastry TB Acton B Honig GT Montelione MA Kennedy, J Mol Biol 2004 344 567 583 10.1016/j.jmb.2004.08.038 15522305
26. High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases. G Liu Z Li Y Chiang T Acton GT Montelione D Murray T Szyperski, Protein Sci 2005 14 6 1597 1608 15930006 10.1110/ps.041322705
27. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. IT Paulsen L Banerjei GS Myers KE Nelson R Seshadri TD Read DE Fouts JA Eisen SR Gill JF Heidelberg H Tettelin RJ Dodson L Umayam L Brinkac M Beanan S Daugherty RT DeBoy S Durkin J Kolonay R Madupu W Nelson J Vamathevan B Tran J Upton T Hansen J Shetty H Khouri T Utterback D Radune KA Ketchum BA Dougherty CM Fraser, Science 2003 299 5615 2071 2074 10.1126/science.1080613 12663927
28. Iron-sulfur cluster biosynthesis: Thermatoga maritima IscU is a structured iron-sulfur cluster assembly protein. SS Mansy G Wu KK Surerus JA Cowan, J Biol Chem 2002 277 21397 21404 10.1074/jbc.M201439200 11934893
29. SufE transfers sulfur from SufS to SufB for iron-sulfur cluster assembly. G Layer SA Gaddam CN Ayala-Castro S Ollagnier-de Choudens D Lascoux M Fontecave FW Outten, J Biol Chem 2007 282 18 13342 50 10.1074/jbc.M608555200 17350958
30. The SufE protein and the SufBCD complex enhance SufS cysteine desulfurase activity as part of a sulfur transfer pathway for Fe-S cluster assembly in Escherichia coli. FW Outten MJ Wood FM Munoz G Storz, J Biol Chem 2003 278 46 45713 45719 10.1074/jbc.M308004200 12941942
31. 2+,1+ clusters and functions as a transcriptional repressor of the sufBCDS operon and an autoregulator of sufR in cyanobacteria. G Shen R Balasubramanian T Wang Y Wu LM Hoffart C Krebs DA Bryant JH Golbeck, J Biol Chem 2007 282 44 31909 31919 10.1074/jbc.M705554200 17827500
32. Mimicking the action of folding chaperones in molecular dynamics simulations: Application to the refinement of homology-based protein structures. H Fan AE Mark, Protein Sci 2004 13 4 992 9 15010545 10.1110/ps.03449904
33. Formation and properties of [4Fe-4S] clusters on the IscU scaffold protein. K Chandramouli MC Unciuleac S Naik DR Dean BH Huynh MK Johnson, Biochemistry 2007 46 23 6804 6811 10.1021/bi6026659 17506525
34. Modeling and Molecular Dynamics Simulation of the Human Gonadotropin-Releasing Hormone Receptor in a Lipid Bilayer. E Jardán-Valadez A Ulloa-Aguirre A Pĩeiro, J Phys Chem B 2008 112 34 10704 13 10.1021/jp800544x 18680336
35. Structural refinement of membrane proteins by restrained molecular dynamics and solvent accessibility data. P Sompornpisut B Roux E Perozo, Biophys J 95 11 5349 5361 18676641 10.1529/biophysj.108.142984
36. Insights into the induced fit mechanism in antithrombin-heparin interaction using molecular dynamics simulations. H Verli JA Guimarães, J Mol Graph Model 2005 24 3 203 12 10.1016/j.jmgm.2005.07.002 16146701
37. Structural and functional behavior of biologically active monomeric melittin. RM Terra JA Guimarães H Verli, J Mol Graph Model 2007 25 6 767 772 10.1016/j.jmgm.2006.06.006 16905347
38. Molecular dynamics analysis of HIV-1 matrix protein: Clarifying differences between crystallographic and solution structures. H Verli A Calazans R Brindeiro A Tanuri JA Guimarães, J Mol Graph Model 2007 26 62 68 10.1016/j.jmgm.2006.09.009 17067836
39. Hsc66 substrate specificity is directed toward a discrete region of the [Fe-S] cluster template protein IscU. KG Hoff DT Ta TL Tapley JJ Silberg LE Vickery, J Biol Chem 2002 277 27353 27359 10.1074/jbc.M202814200 11994302
40. HscA and HscB Stimulate [2Fe-2S] Cluster Transfer from IscU to Apoferredoxin in an ATP-Dependent Reaction. K Chandramouli MK Johnson, Biochemistry 2006 45 11087 11095 16964969 10.1021/bi061237w
41. GROMACS - a message-passing parallel molecular-dynamics implementation. HJC Berendsen D van der Spoel R van Drunen, Comput Phys Commun 1985 91 43 56 10.1016/0010-4655(95)00042-E
42. GROMACS User Manual Version 3.2. D van der Spoel E Lindahl B Hess AR van Buuren E Apol PJ Meulenhoff DP Tieleman ALTM Sijbers KA Feenstra R van Drunen HJC Berendsen, Nijenborgh 4, 9747 AG Groningen, The Netherlands 2004
43. Swiss-model and the Swiss-Pdb Viewer: and environment for comparative protein modeling. N Guex MC Peitsch, Electrophoresis 1997 18 2714 2723 10.1002/elps.1150181505 9504803
44. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. W Kabsch C Sander, Biopolymers 1983 22 2577 2637 10.1002/bip.360221211 6667333
45. The PyMOL Molecular Graphics System. WL DeLano, DeLano Scientific, Sao Carlos, CA, USA 2002
46. Molecular dynamics with coupling to an external bath. HJC Berendsen JPM Postma A DiNola JR Haak, J Chem Phys 1984 81 3684 3690 10.1063/1.448118