Co-repressor induced order and biotin repressor dimerization: A case for divergent followed by convergent evolution

Journal of Molecular Biology

Volumn 357, Issue 2, 2006, Pages 509-523

  Wood, Zachary A ^a   Weaver, Larry H ^a   Brown, Patrick H ^b   Beckett, Dorothy ^b   Matthews, Brian W ^a  

^a UNIVERSITY OF OREGON   (United States)

^b Bldg 142   (United States)

Author keywords

Biotin repressor; Class II tRNA synthetases; Evolution; Lipoate; Order to disorder

Indexed keywords

AMINO ACID; AMINO ACID TRANSFER RNA LIGASE; BIOTIN; ENZYME; LIPOATE PROTEIN LIGASE; NUCLEOTIDE; PROTEIN; PROTEIN BIRA; THIOCTIC ACID; UNCLASSIFIED DRUG;

ADENYLATION; ARTICLE; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DIMERIZATION; PRIORITY JOURNAL; PROTEIN BINDING; STRUCTURE ANALYSIS;

EID: 33344466006     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.12.066     Document Type: Article

References (38)

1. D.F. Barker, and A.M. Campbell Genetic and biochemical characterization of the birA gene and its product: evidence for a direct role of biotin holoenzyme synthetase in repression of the biotin operon J. Mol. Biol. 146 1981 469 492
2. M.A. Eisenberg, O. Prakash, and S. Hsiung Purification and properties of the biotin repressor. A bifunctional protein J. Biol. Chem. 257 1982 15167 15173
3. A. Chapman-Smith, and J.E. Cronan Jr The enzymatic biotinylation of proteins: a post-translational modification of exceptional specificity Trends Biochem. Sci. 24 1999 359 363
4. E. Eisenstein, and D. Beckett Dimerization of the Escherichia coli biotin repressor: corepressor function in protein assembly Biochemistry 38 1999 13077 13084
5. E.D. Streaker, and D. Beckett Coupling of protein assembly and DNA binding: biotin repressor dimerization precedes biotin operator binding J. Mol. Biol. 325 2003 937 948
6. K.P. Wilson, L.M. Shewchuk, R.G. Brennan, A.J. Otsuka, and B.W. Matthews Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains Proc. Natl Acad. Sci. USA 89 1992 9257 9261
7. L.H. Weaver, K. Kwon, D. Beckett, and B.W. Matthews Co-repressor-induced organization and assembly of the biotin repressor: a model for allosteric activation of a transcriptional regulator Proc. Natl Acad. Sci. USA 98 2001 6045 6050
8. A. Chapman-Smith, T.D. Mulhern, F. Whelan, J.E. Cronan Jr, and J.C. Wallace The C-terminal domain of biotin protein ligase from E. coli is required for catalytic activity Protein Sci. 10 2001 2608 2617
9. L.H. Weaver, K. Kwon, D. Beckett, and B.W. Matthews Competing protein:protein interactions are proposed to control the biological switch of the E. coli biotin repressor Protein Sci. 10 2001 2618 2622
10. E.D. Streaker, A. Gupta, and D. Beckett The biotin repressor: thermodynamic coupling of co-repressor binding, protein assembly, and sequence-specific DNA binding Biochemistry 41 2002 14263 14271
11. C.R. Bellamacina The nicotinamide dinucleotide binding motif: a comparison of nucleotide binding proteins FASEB J. 10 1996 1257 1269
12. K. Kwon, E.D. Streaker, S. Ruparelia, and D. Beckett Multiple disordered loops function in co-repressor-induced dimerization of the biotin repressor J. Mol. Biol. 304 2000 821 833
13. K. Kwon, and D. Beckett Function of a conserved sequence motif in biotin holoenzyme synthetases Protein Sci. 9 2000 1530 1539
14. K. Kwon, E.D. Streaker, and D. Beckett Binding specificity and the ligand dissociation process in the E. coli biotin holoenzyme synthetase Protein Sci. 11 2002 558 570
15. E.D. Streaker, and D. Beckett Ligand-linked structural changes in the Escherichia coli biotin repressor: the significance of surface loops for binding and allostery J. Mol. Biol. 292 1999 619 632
16. B. Bagautdinov, C. Kuroishi, M. Sugahara, and N. Kunishima Crystal structures of biotin protein ligase from Pyrococcus horikoshiii OT3 and its complexes: structural basis of biotin activation J. Mol. Biol. 353 2005 322 333
17. P.H. Brown, J.E. Cronan, M. Grotli, and D. Beckett The biotin repressor: modulation of allostery by co-repressor analogs J. Mol. Biol. 337 2004 857 869
18. Y. Xu, and D. Beckett Kinetics of biotinyl-5′-adenylate synthesis catalyzed by the Escherichia coli repressor of biotin biosynthesis and the stability of the enzyme-product complex Biochemistry 33 1994 7354 7360
19. Y. Chen, and G. Varani Protein families and RNA recognition FEBS J. 272 2005 2088 2097
20. M. Delarue, A. Poterszman, S. Nikonov, M. Garber, D. Moras, and J.C. Thierry Crystal structure of a prokaryotic aspartyl tRNA-synthetase EMBO J. 13 1994 3219 3229
21. J. Abendroth, A.E. Rice, K. McLuskey, M. Bagdasarian, and W.G. Hol The crystal structure of the periplasmic domain of the type II secretion system protein EpsM from Vibrio cholerae: the simplest version of the ferredoxin fold J. Mol. Biol. 338 2004 585 596
22. P.A. Reche Lipoylating and biotinylating enzymes contain a homologous catalytic module Protein Sci. 9 2000 1922 1929
23. D.J. Kim, K.H. Kim, H.H. Lee, S.J. Lee, J.Y. Ha, H.J. Yoon, and S.W. Suh Crystal structure of lipoate-protein ligase A bound with the activated intermediate: Insights into interaction with lipoyl domains J. Biol. Chem. 280 2005 38081 38088
24. P.J. Artymiuk, D.W. Rice, A.R. Poirrette, and P. Willet A tale of two synthetases Nature Struct. Biol. 1 1994 758 760
25. M. Safro, and L. Mosyak Structural similarities in the noncatalytic domains of phenylalanyl-tRNA and biotin synthetases Protein Sci. 4 1995 2429 2432
26. F. Pan, K.Y. Lo, S.H. Pai, and H.H. Lee Kinetic mechanism of threonyl-tRNA synthetase from human placenta Int. J. Pept. Protein Res. 20 1982 159 166
27. G.M. Nagel, and R.F. Doolittle Evolution and relatedness in to aminoacyl-tRNA synthetase families Proc. Natl Acad. Sci. USA 88 1991 121 125
28. J. Kuriyan, T.S. Krishna, L. Wong, B. Guenther, A. Pahler, C.H. Williams Jr, and P. Model Convergent evolution of similar function in two structurally divergent enzymes Nature 352 1991 172 174
29. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1996 307 326
30. K. Diederichs, and P.A. Karplus Improved R-factors for diffraction data analysis in macromolecular crystallography Nature Struct. Biol. 4 1997 269 275 (Published erratum appears in Nature Struct. Biol. (1997) 4(7), 592)
31. A.T. Brunger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, and R.W. Grosse-Kunstleve Crystallography and NMR system: a new software suite for macromolecular structure determination Acta Crystallog. sect. D 54 1998 905 921
32. A.T. Brunger Free R value: cross-validation in crystallography Methods Enzymol. 277B 1997 366 396
33. T.A. Jones, J.Y. Zou, S.W. Cowan, and M. Kjeldgaard Improved methods for building protein models in electron density and the location of errors in these models Acta Crystallog. 47 1991 110 119
34. S. Hayward, and H.J. Berendsen Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme Proteins: Struct. Funct. Genet. 30 1998 144 154
35. D.R. Westhead, T.W. Slidel, T.P. Flores, and J.M. Thornton Protein structural topology: automated analysis and diagrammatic representation Protein Sci. 8 1999 897 904
36. L. Holm, and C. Sander Protein structure comparison by alignment of distance matrices J. Mol. Biol. 233 1993 123 138
37. Collaborative Computational Project, No. 4 The CCP4 Suite: programs for protein crystallography. Acta Crystallog. sect. D 50 1994 760 763
38. A.C. Wallace, R.A. Laskowski, and J.M. Thornton LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions Protein Eng. 8 1995 127 134