Structural and functional characteristics of xenavidin, the first frog avidin from Xenopus tropicalis

BMC Structural Biology

Volumn 9, Issue , 2009, Pages

  Määttä, Juha Ae ^a   Helppolainen, Satu H ^a   Hytönen, Vesa P ^a   Johnson, Mark S ^b   Kulomaa, Markku S ^a   Airenne, Tomi T ^b   Nordlund, Henri R ^a  

^a UNIVERSITY OF TAMPERE   (Finland)

^b ÅBO AKADEMI UNIVERSITY   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

AVIDIN; BIOTIN; INSECT PROTEIN; STREPTAVIDIN; UNCLASSIFIED DRUG; XENAVIDIN; LIGAND; RECOMBINANT PROTEIN;

ARTICLE; BINDING SITE; BIOCHEMISTRY; CONTROLLED STUDY; GEL FILTRATION; MOLECULAR CLONING; PHYSICAL CHEMISTRY; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN PURIFICATION; PROTEIN STABILITY; PROTEIN STRUCTURE; X RAY CRYSTALLOGRAPHY; XENOPUS; XENOPUS TROPICALIS; AMINO ACID SEQUENCE; ANIMAL; CHEMISTRY; METABOLISM; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

ANURA; BACTERIA (MICROORGANISMS); HEXAPODA; XENOPUS TROPICALIS;

AMINO ACID SEQUENCE; ANIMALS; AVIDIN; BINDING SITES; BIOTIN; CRYSTALLOGRAPHY, X-RAY; LIGANDS; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; XENOPUS;

EID: 70350268430     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-9-63     Document Type: Article

References (69)

1. Occurrence of avidin in the oviduct and secretions of the genital tract of several species. R Hertz WH Sebrell, Science 1942 96 257 10.1126/science.96. 2489.257 17770530
2. Induction of avidin synthesis by RNA obtained from lizard oviducts. V Botte G Granata, J Endocrinol 1977 73 535 536 10.1677/joe.0.0730535 874405
3. Avidin induction by estrogen and progesterone in the immature oviduct of chicken, Japanese Quail, duck and gull. JK Korpela HA Elo PJ Tuohimaa, Gen Comp Endocr 1981 44 230 232 10.1016/0016-6480(81)90253-7 7250686
4. Biotin-binding proteins in eggs of oviparous vertebrates. JK Korpela MS Kulomaa HA Elo PJ Tuohimaa, Experientia 1981 37 1065 1066 10.1007/BF02085010 7308390
5. Comparison of avidin and biotin levels in eggs from turkey hens with high and low hatchability records. EJ Robel, Comp Biochem Physiol B 1987 86 265 267 10.1016/0305-0491(87)90289-6 3568617
6. The occurrence and production of avidin: a new conception of the high-affinity biotin-binding protein. HA Elo J Korpela, Comp Biochem Physiol B 1984 78 15 20 10.1016/0305-0491(84)90137-8 6086227
7. The properties of streptavidin, a biotin-binding protein produced by Streptomycetes. L Chaiet FJ Wolf, Arch Biochem Biophys 1964 106 1 5 10.1016/0003-9861(64)90150-X 14217155
8. Close similarity among streptavidin-like, biotin-binding proteins from Streptomyces. EA Bayer T Kulik R Adar M Wilchek, Biochim Biophys Acta 1995 1263 60 66 7632734
9. Novel avidin-like protein from a root nodule symbiotic bacterium, Bradyrhizobium japonicum. HR Nordlund VP Hytönen OH Laitinen MS Kulomaa, J Biol Chem 2005 280 13250 13255 10.1074/jbc.M414336200 15695809
10. Rhizavidin from Rhizobium etli: the first natural dimer in the avidin protein family. SH Helppolainen KP Nurminen JA Määttä KK Halling JP Slotte T Huhtala T Liimatainen S Ylä-Herttuala KJ Airenne A Narvanen, et al. Biochem J 2007 405 397 405 10.1042/BJ20070076 17447892
11. The avidin-biotin complex in bioanalytical applications. M Wilchek EA Bayer, Anal Biochem 1988 171 1 32 10.1016/0003-2697(88)90120-0 3044183
12. Genetically engineered avidins and streptavidins. OH Laitinen VP Hytönen HR Nordlund MS Kulomaa, Cell Mol Life Sci 2006 63 2992 3017 10.1007/s00018-006-6288-z 17086379
13. Characterization of poultry egg-white avidins and their potential as a tool in pretargeting cancer treatment. VP Hytönen OH Laitinen A Grapputo A Kettunen J Savolainen N Kalkkinen AT Marttila HR Nordlund TK Nyholm G Paganelli MS Kulomaa, Biochem J 2003 372 219 225 10.1042/BJ20021531 12558501
14. Chicken avidin-related protein 4/5 shows superior thermal stability when compared with avidin while retaining high affinity to biotin. VP Hytönen TK Nyholm OT Pentikäinen J Vaarno EJ Porkka HR Nordlund MS Johnson JP Slotte OH Laitinen MS Kulomaa, J Biol Chem 2004 279 9337 9343 10.1074/jbc.M310989200 14660583
15. Structure and characterization of a novel chicken biotin-binding protein A (BBP-A). VP Hytönen JA Määttä EA Niskanen J Huuskonen KJ Helttunen KK Halling HR Nordlund K Rissanen MS Johnson TA Salminen, et al. BMC Struct Biol 2007 7 8 10.1186/1472-6807-7-8 17343730
16. Design and construction of highly stable, protease-resistant chimeric avidins. VP Hytönen JA Määttä TK Nyholm O Livnah Y Eisenberg-Domovich D Hyre HR Nordlund J Hörhä EA Niskanen T Paldanius, et al. J Biol Chem 2005 280 10228 10233 10.1074/jbc.M414196200 15649900
17. Structural origins of high-affinity biotin binding to streptavidin. PC Weber DH Ohlendorf JJ Wendoloski FR Salemme, Science 1989 243 85 88 10.1126/science.2911722 2911722
18. Three-dimensional structures of avidin and the avidin-biotin complex. O Livnah EA Bayer M Wilchek JL Sussman, Proc Natl Acad Sci USA 1993 90 5076 5080 10.1073/pnas.90.11.5076 8506353
19. Three-dimensional structure of the tetragonal crystal form of egg-white avidin in its functional complex with biotin at 2.7 resolution. L Pugliese A Coda M Malcovati M Bolognesi, J Mol Biol 1993 231 698 710 10.1006/jmbi.1993.1321 8515446
20. Avidin related protein 2 shows unique structural and functional features among the avidin protein family. VP Hytönen JA Määttä H Kidron KK Halling J Hörha T Kulomaa TK Nyholm MS Johnson TA Salminen MS Kulomaa TT Airenne, BMC Biotechnol 2005 5 28 10.1186/1472-6750-5-28 16212654
21. High-resolution crystal structure of an avidin-related protein: insight into high-affinity biotin binding and protein stability. Y Eisenberg-Domovich VP Hytönen M Wilchek EA Bayer MS Kulomaa O Livnah, Acta Crystallogr D 2005 61 528 538 10.1107/S0907444905003914 15858262
22. Xenopus, the next generation: X. tropicalis genetics and genomics. N Hirsch LB Zimmerman RM Grainger, Dev Dyn 2002 225 422 433 10.1002/dvdy.10178 12454920
23. Genetic and genomic prospects for Xenopus tropicalis research. S Carruthers DL Stemple, Semin Cell Dev Biol 2006 17 146 153 10.1016/j.semcdb. 2005.11.009 16427790 (Pubitemid 43344471)
24. dbEST-database for "expressed sequence tags". MS Boguski TM Lowe CM Tolstoshev, Nat Genet 1993 4 332 333 10.1038/ng0893-332 8401577
25. Efficient production of active chicken avidin using a bacterial signal peptide in Escherichia coli. VP Hytönen OH Laitinen TT Airenne H Kidron NJ Meltola E Porkka J Hörhä T Paldanius JA Määttä HR Nordlund, et al. Biochem J 2004 384 385 390 10.1042/BJ20041114 15324300
26. Thermodynamic and structural consequences of flexible loop deletion by circular permutation in the streptavidin-biotin system. V Chu S Freitag I Le Trong RE Stenkamp PS Stayton, Protein Sci 1998 7 848 859 9568892
27. Binding properties of HABA-type azo derivatives to avidin and avidin-related protein 4. S Repo TA Paldanius VP Hytönen TK Nyholm KK Halling J Huuskonen OT Pentikäinen K Rissanen JP Slotte TT Airenne, et al. Chem Biol 2006 13 1029 1039 10.1016/j.chembiol.2006.08.006 17052607
28. Rational modification of ligand-binding preference of avidin by circular permutation and mutagenesis. JA Määttä TT Airenne HR Nordlund J Jänis TA Paldanius P Vainiotalo MS Johnson MS Kulomaa VP Hytönen, Chembiochem 2008 9 1124 1135 10.1002/cbic.200700671 18381715
29. Cooperative biotin binding by streptavidin. Electrophoretic behavior and subunit association of streptavidin in the presence of 6 M urea. T Sano CR Cantor, J Biol Chem 1990 265 3369 3373 2406253
30. (Strept)avidin as host for biotinylated coordination complexes: stability, chiral discrimination, and cooperativity. A Loosli UE Rusbandi J Gradinaru K Bernauer CW Schlaepfer M Meyer S Mazurek M Novic TR Ward, Inorg Chem 2006 45 660 668 10.1021/ic051405t 16411701
31. Noncooperativity of biotin binding to tetrameric streptavidin. ML Jones GP Kurzban, Biochemistry 1995 34 11750 11756 10.1021/bi00037a012 7547907
32. Interaction of biotin with streptavidin. Thermostability and conformational changes upon binding. M Gonzalez LA Bagatolli I Echabe JLR Arrondo CE Argarana CR Cantor GD Fidelio, J Biol Chem 1997 25 11288 11294
33. Early mechanistic events in biotin dissociation from streptavidin. DE Hyre LM Amon JE Penzotti I Le Trong RE Stenkamp TP Lybrand PS Stayton, Nat Struct Biol 2002 9 582 585 12134141
34. X-ray crystallographic studies of streptavidin mutants binding to biotin. S Freitag I Le Trong LA Klumb V Chu A Chilkoti PS Stayton RE Stenkamp, Biomol Eng 1999 16 13 19 10.1016/S1050-3862(99)00048-0 10796980
35. Cooperative hydrogen bond interactions in the streptavidin-biotin system. DE Hyre I Le Trong EA Merritt JF Eccleston NM Green RE Stenkamp PS Stayton, Protein Sci 2006 15 459 467 10.1110/ps.051970306 16452627
36. Advances in the use of recombinant baculoviruses for the expression of heterologous proteins. AH Davies, Curr Opin Biotech 1995 6 543 547 10.1016/0958-1669(95)80090-5
37. Chicken avidin-related proteins show altered biotin-binding and physico-chemical properties as compared with avidin. OH Laitinen VP Hytönen MK Ahlroth OT Pentikäinen C Gallagher HR Nordlund V Ovod AT Marttila E Porkka S Heino, et al. Biochem J 2002 363 609 617 10.1042/0264-6021:3630609 11964162
38. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. B Bjellqvist GJ Hughes C Pasquali N Paquet F Ravier JC Sanchez S Frutiger D Hochstrasser, Electrophoresis 1993 14 1023 1031 10.1002/elps.11501401163 8125050
39. Bradavidin II from Bradyrhizobium japonicum: a new avidin-like biotin-binding protein. SH Helppolainen JA Määttä KK Halling JP Slotte VP Hytönen J Jänis P Vainiotalo MS Kulomaa HR Nordlund, Biochim Biophys Acta 2008 1784 1002 1010 18486632
40. Sodium dodecyl sulfate-polyacrylamide gel electrophoretic method for assessing the quaternary state and comparative thermostability of avidin and streptavidin. EA Bayer S Ehrlich-Rogozinski M Wilchek, Electrophoresis 1996 17 1319 1324 10.1002/elps.1150170808 8874057
41. Limited proteolysis of native proteins: the interaction between avidin and proteinase K. D Ellison J Hinton SJ Hubbard RJ Beynon, Protein Sci 1995 4 1337 1345 10.1002/pro.5560040709 7670376
42. Ligand exchange between proteins. Exchange of biotin and biotin derivatives between avidin and streptavidin. Y Pazy T Kulik EA Bayer M Wilchek O Livnah, J Biol Chem 2002 277 30892 30900 10.1074/jbc.M202874200 12055191
43. Avidin, a high affinity biotin-binding protein as a tool and subject of biological reserch. J Korpela, Medical Biology 1984 62 5 26 6379329
44. Induction of chicken avidin and related mRNAs after bacterial infection. TA Kunnas MJ Wallén MS Kulomaa, Biochim Biophys Acta 1993 1216 441 445 8268225
45. Immunobiological studies of the jelly-coats of anuran eggs. JR Shaver, Am Zool 1966 6 75 87 5902514
46. Tamavidins-novel avidin-like biotin-binding proteins from the Tamogitake mushroom. Y Takakura M Tsunashima J Suzuki S Usami Y Kakuta N Okino M Ito T Yamamoto, FEBS J 2009 276 1383 1397 10.1111/j.1742-4658.2009.06879.x 19187241
47. Pharmacokinetics and biodistribution of radiolabeled avidin, streptavidin and biotin. SF Rosebrough, Nucl Med Biol 1993 20 663 668 10.1016/0969-8051(93) 90037-U 8358353
48. Avidin-biotin system for delivery of diagnostic agents. H Sakahara T Saga, Adv Drug Deliv Rev 1999 37 89 101 10.1016/S0169-409X(98)00101-X 10837729
49. Tissue distribution of avidin and streptavidin injected to mice. Effect of avidin carbohydrate, streptavidin truncation and exogenous biotin. B Schechter R Silberman R Arnon M Wilchek, Eur J Biochem 1990 189 327 331 10.1111/j.1432-1033.1990.tb15493.x 2186907
50. Biochemical modification of streptavidin and avidin: in vitro and in vivo analysis. SF Rosebrough DF Hartley, J Nucl Med 1996 37 1380 1384 8708779
51. Avidin targeting of intraperitoneal tumor xenografts. Z Yao M Zhang H Sakahara T Saga Y Arano J Konishi, J Natl Cancer Inst 1998 90 25 29 10.1093/jnci/90.1.25 9428779
52. The relationship of glycosylation and isoelectric point with tumor accumulation of avidin. Z Yao M Zhang H Sakahara Y Nakamoto T Higashi S Zhao N Sato Y Arano J Konishi, J Nucl Med 1999 40 479 483 10086714
53. Use of neutral avidin improves pharmacokinetics and brain delivery of biotin bound to an avidin-monoclonal antibody conjugate. Y-S Kang WM Pardridge, J Pharmacol Exp Ther 1994 269 344 350 8169841
54. Production of biologically active recombinant avidin in baculovirus-infected insect cells. KJ Airenne C Oker-Blom VS Marjomäki EA Bayer M Wilchek MS Kulomaa, Protein Expr Purif 1997 9 100 108 10.1006/prep.1996.0660 9116491
55. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. W Kabsch, J Appl Crystallogr 1993 26 795 800 10.1107/S0021889893005588
56. Likelihood-enhanced fast translation functions. AJ McCoy RW Grosse-Kunstleve LC Storoni RJ Read, Acta Crystallogr D Biol Crystallogr 2005 61 458 464 10.1107/S0907444905001617 15805601
57. The CCP4 suite: programs for protein crystallography. Collaborative Computational Project, Number 4, Acta Crystallogr D Biol Crystallogr 1994 50 760 763 10.1107/S0907444994003112 15299374
58. A graphical user interface to the CCP4 program suite. E Potterton P Briggs M Turkenburg E Dodson, Acta Crystallogr D Biol Crystallogr 2003 59 1131 1137 10.1107/S0907444903008126 12832755
59. Automated protein model building combined with iterative structure refinement. A Perrakis R Morris VS Lamzin, Nat Struct Biol 1999 6 458 463 10.1038/8263 10331874
60. Refinement of macromolecular structures by the maximum-likelihood method. GN Murshudov AA Vagin EJ Dodson, Acta Crystallogr D 1997 53 240 255 10.1107/S0907444996012255 15299926
61. Coot: model-building tools for molecular graphics. P Emsley K Cowtan, Acta Crystallogr D 2004 60 2126 2132 10.1107/S0907444904019158 15572765
62. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. MD Winn MN Isupov GN Murshudov, Acta Crystallogr D Biol Crystallogr 2001 57 122 133 10.1107/S0907444900014736 11134934
63. Energetic roles of hydrogen bonds at the ureido oxygen binding pocket in the streptavidin-biotin complex. LA Klumb V Chu PS Stayton, Biochemistry 1998 37 7657 7663 10.1021/bi9803123 9601024
64. Mutation of a critical tryptophan to lysine in avidin or streptavidin may explain why sea urchin fibropellin adopts an avidin-like domain. OH Laitinen KJ Airenne AT Marttila T Kulik E Porkka EA Bayer M Wilchek MS Kulomaa, FEBS Lett 1999 461 52 58 10.1016/S0014-5793(99)01423-4 10561495
65. The PyMOL molecular graphics system. WL DeLano, DeLano Scientific LLC, Palo Alto, CA, USA 2008
66. BODIL: a molecular modeling environment for structure-function analysis and drug design. JV Lehtonen DJ Still VV Rantanen J Ekholm D Björklund Z Iftikhar M Huhtala S Repo A Jussila J Jaakkola, et al. J Comput Aided Mol Des 2004 18 401 419 10.1007/s10822-004-3752-4 15663001
67. ESPript: analysis of multiple sequence alignments in PostScript. P Gouet E Courcelle DI Stuart F Metoz, Bioinformatics 1999 15 305 308 10.1093/bioinformatics/15.4.305 10320398
68. Electrostatics of nanosystems: application to microtubules and the ribosome. NA Baker D Sept S Joseph MJ Holst JA McCammon, Proc Natl Acad Sci USA 2001 98 10037 10041 10.1073/pnas.181342398 11517324
69. Egg white avidin. I. Amino acid composition; sequence of the amino- and carboxyl-terminal cyanogen bromide peptides. RJ DeLange, J Biol Chem 1970 245 907 916 5417264