Model structures of helicobacter pylori UreD(H) domains: A putative molecular recognition platform

Journal of Chemical Information and Modeling

Volumn 51, Issue 7, 2011, Pages 1513-1520

  Musiani, Francesco ^a   Bellucci, Matteo ^a,c   Ciurli, Stefano ^a,b  

^a UNIVERSITY OF BOLOGNA   (Italy)

^b UNIVERSITY OF FLORENCE   (Italy)

^c CENTRE FOR GENOMIC REGULATION CRG   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATION ANALYSIS; BINDING SITES; MODEL STRUCTURES; MOLECULAR RECOGNITION; PHYSICOCHEMICAL PROPERTIES;

ACTIVE SITE; HELICOBACTER PYLORI; MODEL ALGORITHMS; PROTEIN SURFACE; PUTATIVE BINDING SITES; SEQUENCE CONSERVATION; STRUCTURAL SIMILARITY; TWO DOMAINS;

PROTEINS;

BACTERIAL PROTEIN; UREASE; URED PROTEIN, BACTERIA;

AMINO ACID SEQUENCE; ARTICLE; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME ACTIVATION; ENZYME ACTIVE SITE; GENETICS; HELICOBACTER PYLORI; METABOLISM; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; SOLUBILITY;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CATALYTIC DOMAIN; ENZYME ACTIVATION; HELICOBACTER PYLORI; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SOLUBILITY; UREASE;

EID: 79960733016     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci200183n     Document Type: Article

References (65)

1. Finney, L. A.; O'Halloran, T. V. Transition metal speciation in the cell: insights from the chemistry of metal ion receptors Science 2003, 300, 931-936 (Pubitemid 36548870)
2. Giedroc, D. P.; Arunkumar, A. I. Metal sensor proteins: nature's metalloregulated allosteric switches Dalton Trans. 2007, 3107-3120 (Pubitemid 47117766)
3. Ciurli, S. In Biological Inorganic Chemistry: Structure & Reactivity; Bertini, I.; Gray, H. B.; Valentine, J. S., Eds.; University Science Books: Sausalito, CA, 2007, p 198-208.
4. Ciurli, S. In Nickel and its surprising role in nature; Sigel, A.; Sigel, H.; Sigel, R. K. O., Eds.; Wiley & Sons, Ltd.: Chichester, U.K., 2007, p 241-278.
5. Zanotti, G.; Cendron, L. Functional and structural aspects of Helicobacter pylori acidic stress response factors IUBMB Life 2010, 62, 715-723
6. Jabri, E.; Carr, M. B.; Hausinger, R. P.; Karplus, P. A. The crystal structure of urease from Klebsiella aerogenes Science 1995, 268, 998-1004
7. Benini, S.; Rypniewski, W. R.; Wilson, K. S.; Miletti, S.; Ciurli, S.; Mangani, S. A new proposal for urease mechanism based on the crystal structures of the native and inhibited enzyme from Bacillus pasteurii: why urea hydrolysis costs two nickels Structure 1999, 7, 205-216 (Pubitemid 29159705)
8. Ha, N. C.; Oh, S. T.; Sung, J. Y.; Cha, K. A.; Lee, M. H.; Oh, B. H. Supramolecular assembly and acid resistance of Helicobacter pylori urease Nat. Struct. Biol. 2001, 8, 505-509 (Pubitemid 32525008)
9. Balasubramanian, A.; Ponnuraj, K. Crystal structure of the first plant urease from jack bean: 83 years of journey from its first crystal to molecular structure J. Mol. Biol. 2010, 400, 274-283
10. Musiani, F.; Arnofi, E.; Casadio, R.; Ciurli, S. Structure-based computational study of the catalytic and inhibition mechanisms of urease J. Biol. Inorg. Chem. 2001, 6, 300-314 (Pubitemid 32825512)
11. Quiroz, S.; Kim, J. K.; Mulrooney, S. B.; Hausinger, R. P. In Nickel and its surprising role in nature; Sigel, A.; Sigel, H.; Sigel, R. K. O., Eds.; Wiley & Sons, Ltd.: Chichester, UK, 2007, p 519-544.
12. Kaluarachchi, H.; Chan Chung, K. C.; Zamble, D. B. Microbial nickel proteins Nat. Prod. Rep. 2010, 27, 681-694
13. Zambelli, B.; Turano, P.; Musiani, F.; Neyroz, P.; Ciurli, S. Zn2+-linked dimerization of UreG from Helicobacter pylori, a chaperone involved in nickel trafficking and urease activation Proteins 2009, 74, 222-239
14. Salomone-Stagni, M.; Zambelli, B.; Musiani, F.; Ciurli, S. A model-based proposal for the role of UreF as a GTPase-activating protein in the urease active site biosynthesis Proteins 2007, 68, 749-761 (Pubitemid 47068313)
15. Lam, R.; Romanov, V.; Johns, K.; Battaile, K. P.; Wu-Brown, J.; Guthrie, J. L.; Hausinger, R. P.; Pai, E. F.; Chirgadze, N. Y. Crystal structure of a truncated urease accessory protein UreF from Helicobacter pylori Proteins 2010, 78, 2839-2848
16. Park, I.-S.; Hausinger, R. P. Metal ion interactions with urease and UreD-urease apoproteins Biochemistry 1996, 35, 5345-5352 (Pubitemid 26129477)
17. Park, I. S.; Hausinger, R. P. Requirement of carbon dioxide for in vitro assembly of the urease nickel metallocenter Science 1995, 267, 1156-1158
18. Soriano, A.; Colpas, G. J.; Hausinger, R. P. UreE stimulation of GTP-dependent urease activation in the UreD-UreF-UreG-urease apoprotein complex Biochemistry 2000, 39, 12435-12440
19. Rain, J. C.; Selig, L.; De Reuse, H.; Battaglia, V.; Reverdy, C.; Simon, S.; Lenzen, G.; Petel, F.; Wojcik, J.; Schachter, V.; Chemama, Y.; Labigne, A.; Legrain, P. The protein-protein interaction map of Helicobacter pylori Nature 2001, 409, 211-215 (Pubitemid 32144288)
20. Voland, P.; Weeks, D. L.; Marcus, E. A.; Prinz, C.; Sachs, G.; Scott, D. Interactions among the seven Helicobacter pylori proteins encoded by the urease gene cluster Am. J. Physiol. Gastrointest. Liver Physiol. 2003, 284, G96-G106
21. Bellucci, M.; Zambelli, B.; Musiani, F.; Turano, P.; Ciurli, S. Helicobacter pylori UreE, a urease accessory protein: specific Ni2+- and Zn2+-binding properties and interaction with its cognate UreG Biochem. J. 2009, 422, 91-100
22. Lee, M. H.; Mulrooney, S. B.; Renner, M. J.; Markowicz, Y.; Hausinger, R. P. Klebsiella aerogenes urease gene cluster: sequence of ureD and demonstration that four accessory genes (ureD, ureE, ureF, ureG) are involved in nickel metallocenter biosynthesis J. Bacteriol. 1992, 174, 4324-4330
23. Park, I. S.; Carr, M. B.; Hausinger, R. P. In vitro activation of urease apoprotein and role of UreD as a chaperone required for nickel metallocenter assembly Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 3233-3237 (Pubitemid 24130210)
24. Park, I. S.; Hausinger, R. P. Evidence for the presence of urease apoprotein complexes containing UreD, UreF, and UreG in cells that are competent for in vivo enzyme activation J. Bacteriol. 1995, 177, 1947-1951
25. Moncrief, M. C.; Hausinger, R. P. Purification and activation properties of UreD-UreF-urease apoprotein complexes J. Bacteriol. 1996, 178, 5417-5421 (Pubitemid 26304374)
26. Moncrief, M. C.; Hausinger, R. P. Characterization of UreG, identification of a UreD-UreF-UreG complex, and evidence suggesting that a nucleotide-binding site in UreG is required for in vivo metallocenter assembly of Klebsiella aerogenes urease J. Bacteriol. 1997, 179, 4081-4086 (Pubitemid 27291034)
27. Soriano, A.; Hausinger, R. P. GTP-dependent activation of urease apoprotein in complex with the UreD, UreF, and UreG accessory proteins Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11140-11144 (Pubitemid 29487347)
28. Heimer, S. R.; Mobley, H. L. Interaction of Proteus mirabilis urease apoenzyme and accessory proteins identified with yeast two-hybrid technology J. Bacteriol. 2001, 183, 1423-1433 (Pubitemid 32107739)
29. Chang, Z.; Kuchar, J.; Hausinger, R. P. Chemical cross-linking and mass spectrometric identification of sites of interaction for UreD, UreF, and urease J. Biol. Chem. 2004, 279, 15305-15313 (Pubitemid 38618928)
30. Quiroz-Valenzuela, S.; Sukuru, S. C.; Hausinger, R. P.; Kuhn, L. A.; Heller, W. T. The structure of urease activation complexes examined by flexibility analysis, mutagenesis, and small-angle X-ray scattering Arch. Biochem. Biophys. 2008, 480, 51-57
31. Kim, J. K.; Mulrooney, S. B.; Hausinger, R. P. The UreEF fusion protein provides a soluble and functional form of the UreF urease accessory protein J. Bacteriol. 2006, 188, 8413-20 (Pubitemid 44894041)
32. Boer, J. L.; Quiroz-Valenzuela, S.; Anderson, K. L.; Hausinger, R. P. Mutagenesis of Klebsiella aerogenes UreG to probe nickel binding and interactions with other urease-related proteins Biochemistry 2010, 49, 5859-69
33. Carter, E. L.; Hausinger, R. P. Characterization of the Klebsiella aerogenes urease accessory protein UreD in fusion with the maltose binding protein J. Bacteriol. 2010, 192, 2294-2304
34. Nomine, Y.; Ristriani, T.; Laurent, C.; Lefevre, J. F.; Weiss, E.; Trave, G. Formation of soluble inclusion bodies by hpv e6 oncoprotein fused to maltose-binding protein Protein Expression Purif. 2001, 23, 22-32 (Pubitemid 32930976)
35. Marsden, R. L.; McGuffin, L. J.; Jones, D. T. Rapid protein domain assignment from amino acid sequence using predicted secondary structure Protein Sci. 2002, 11, 2814-2824 (Pubitemid 35365248)
36. Ginalski, K.; Elofsson, A.; Fischer, D.; Rychlewski, L. 3D-Jury: a simple approach to improve protein structure predictions Bioinformatics 2003, 19, 1015-1018 (Pubitemid 36675823)
37. Chenna, R.; Sugawara, H.; Koike, T.; Lopez, R.; Gibson, T. J.; Higgins, D. G.; Thompson, J. D. Multiple sequence alignment with the Clustal series of programs Nucleic Acids Res. 2003, 31, 3497-3500 (Pubitemid 37442184)
38. Bryson, K.; McGuffin, L. J.; Marsden, R. L.; Ward, J. J.; Sodhi, J. S.; Jones, D. T. Protein structure prediction servers at University College London Nucleic Acids Res. 2005, 33, W36-W38
39. Marti-Renom, M. A.; Stuart, A. C.; Fiser, A.; Sanchez, R.; Melo, F.; Sali, A. Comparative protein structure modeling of genes and genomes Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 291-325 (Pubitemid 30599596)
40. Shen, M. Y.; Sali, A. Statistical potential for assessment and prediction of protein structures Protein Sci. 2006, 15, 2507-2524 (Pubitemid 44771688)
41. Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.; Thornton, J. M. PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 1993, 26, 283-291
42. Wiederstein, M.; Sippl, M. J. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins Nucleic Acids Res. 2007, 35, W407-W410
43. Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. UCSF Chimera-a visualization system for exploratory research and analysis J. Comput. Chem. 2004, 25, 1605-1612
44. Honig, B.; Nicholls, A. Classical electrostatics in biology and chemistry Science 1995, 268, 1144-1149
45. Ashkenazy, H.; Erez, E.; Martz, E.; Pupko, T.; Ben-Tal, N. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids Nucleic Acids Res. 2010, 38, W529-W533
46. Konc, J.; Janezic, D. ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment Bioinformatics 2010, 26, 1160-1168
47. Kent, H. M.; McMahon, H. T.; Evans, P. R.; Benmerah, A.; Owen, D. J. Gamma-adaptin appendage domain: structure and binding site for Eps15 and gamma-synergin Structure 2002, 10, 1139-1148
48. Nogi, T.; Shiba, Y.; Kawasaki, M.; Shiba, T.; Matsugaki, N.; Igarashi, N.; Suzuki, M.; Kato, R.; Takatsu, H.; Nakayama, K.; Wakatsuki, S. Structural basis for the accessory protein recruitment by the gamma-adaptin ear domain Nat. Struct. Biol. 2002, 9, 527-531 (Pubitemid 34693808)
49. Owen, D. J.; Collins, B. M.; Evans, P. R. Adaptors for clathrin coats: structure and function Annu. Rev. Cell Dev. Biol. 2004, 20, 153-191 (Pubitemid 39488636)
50. Boehm, M.; Bonifacino, J. S. Adaptins: the final recount Mol. Biol. Cell 2001, 12, 2907-2920 (Pubitemid 33062950)
51. Robinson, M. S. Adaptable adaptors for coated vesicles Trends Cell. Biol. 2004, 14, 167-174 (Pubitemid 38447116)
52. Steyert, S. R.; Rasko, D. A.; Kaper, J. B. Functional and phylogenetic analysis of ureD in Shiga toxin-producing Escherichia coli J. Bacteriol. 2011, 193, 875-886
53. Brinkman, A. B.; Ettema, T. J.; de Vos, W. M.; van der Oost, J. The Lrp family of transcriptional regulators Mol. Microbiol. 2003, 48, 287-294 (Pubitemid 36819068)
54. Koike, H.; Ishijima, S. A.; Clowney, L.; Suzuki, M. The archaeal feast/famine regulatory protein: potential roles of its assembly forms for regulating transcription Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 2840-2845 (Pubitemid 38327698)
55. Thaw, P.; Sedelnikova, S. E.; Muranova, T.; Wiese, S.; Ayora, S.; Alonso, J. C.; Brinkman, A. B.; Akerboom, J.; van der Oost, J.; Rafferty, J. B. Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family Nucleic Acids Res. 2006, 34, 1439-1449
56. Ren, J.; Sainsbury, S.; Combs, S. E.; Capper, R. G.; Jordan, P. W.; Berrow, N. S.; Stammers, D. K.; Saunders, N. J.; Owens, R. J. The structure and transcriptional analysis of a global regulator from Neisseria meningitidis J. Biol. Chem. 2007, 282, 14655-14664 (Pubitemid 47100439)
57. Nakano, N.; Okazaki, N.; Satoh, S.; Takio, K.; Kuramitsu, S.; Shinkai, A.; Yokoyama, S. Structure of the stand-alone RAM-domain protein from Thermus thermophilus HB8 Acta Crystallogr. 2006, F62, 855-860 (Pubitemid 44357716)
58. Ettema, T. J.; Brinkman, A. B.; Tani, T. H.; Rafferty, J. B.; Van Der Oost, J. A novel ligand-binding domain involved in regulation of amino acid metabolism in prokaryotes J. Biol. Chem. 2002, 277, 37464-37468
59. Konc, J.; Janezic, D. ProBiS: a web server for detection of structurally similar protein binding sites Nucleic Acids Res. 2010, 38, W436-W440
60. Pearse, B. M. Clathrin: a unique protein associated with intracellular transfer of membrane by coated vesicles Proc. Natl. Acad. Sci. U.S.A. 1976, 73, 1255-1259
61. Smith, C. J.; Pearse, B. M. Clathrin: anatomy of a coat protein Trends Cell. Biol. 1999, 9, 335-338 (Pubitemid 29447712)
62. Perez-Torrado, R.; Yamada, D.; Defossez, P. A. Born to bind: the BTB protein-protein interaction domain Bioessays 2006, 28, 1194-1202 (Pubitemid 44925439)
63. Dzhindzhev, N. S.; Yu, Q. D.; Weiskopf, K.; Tzolovsky, G.; Cunha-Ferreira, I.; Riparbelli, M.; Rodrigues-Martins, A.; Bettencourt-Dias, M.; Callaini, G.; Glover, D. M. Asterless is a scaffold for the onset of centriole assembly Nature 2010, 467, 714-718
64. Seiradake, E.; Harlos, K.; Sutton, G.; Aricescu, A. R.; Jones, E. Y. An extracellular steric seeding mechanism for Eph-ephrin signaling platform assembly Nat. Struct. Mol. Biol. 2010, 17, 398-402
65. Farré, J.-C.; Subramani, S. Rallying the exocyst as an autophagy scaffold Cell 2011, 144, 172-174