Crystal structure and centromere binding of the plasmid segregation protein ParB from pCXC100

Nucleic Acids Research

Volumn 39, Issue 7, 2011, Pages 2954-2968

  Huang, Lin ^a,b   Yin, Ping ^a   Zhu, Xing ^b,c   Zhang, Yi ^a   Ye, Keqiong ^b  

^a WUHAN UNIVERSITY   (China)

^b NATIONAL INSTITUTE OF BIOLOGICAL SCIENCES   (China)

^c BEIJING NORMAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; CENTROMERE PROTEIN B;

ARTICLE; BASE PAIRING; BINDING ASSAY; BINDING SITE; CARBOXY TERMINAL SEQUENCE; CENTROMERE; CRYSTAL STRUCTURE; CRYSTALLIZATION; DNA BINDING; DNA PROTEIN COMPLEX; GRAM POSITIVE BACTERIUM; LEIFSONIA XYLI; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS; STOICHIOMETRY; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; BINDING SITES; CENTROMERE; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; DNA-BINDING PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PLASMIDS; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT;

LEIFSONIA XYLI SUBSP. CYNODONTIS; POSIBACTERIA;

EID: 79954585164     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq915     Document Type: Article

References (45)

1. Leonard, T.A., Moller-Jensen, J. and Lowe, J. (2005) Towards understanding the molecular basis of bacterial DNA segregation. Philos. Trans. R. Soc Lond. B Biol. Sci., 360, 523-535. (Pubitemid 41529650)
2. Ebersbach, G. and Gerdes, K. (2005) Plasmid segregation mechanisms. Annu. Rev. Genet., 39, 453-479. (Pubitemid 43011123)
3. Hayes, F. and Barilla, D. (2006) The bacterial segrosome: a dynamic nucleoprotein machine for DNA trafficking and segregation. Nat. Rev. Microbiol., 4, 133-143. (Pubitemid 43158156)
4. Ghosh, S.K., Hajra, S., Paek, A. and Jayaram, M. (2006) Mechanisms for chromosome and plasmid segregation. Annu. Rev. Biochem., 75, 211-241. (Pubitemid 44118032)
5. Schumacher, MA. (2008) Structural biology of plasmid partition: uncovering the molecular mechanisms of DNA segregation. Biochem. J., 412, 1-18. (Pubitemid 351678330)
6. Gerdes, K., Moller-Jensen, J. and Bugge Jensen, R. (2000) Plasmid and chromosome partitioning: surprises from phylogeny. Mol. Microbiol., 37, 455-466. (Pubitemid 30611826)
7. Ni, L., Xu, W., Kumaraswami, M. and Schumacher, MA. (2010) Plasmid protein TubR uses a distinct mode of HTH-DNA binding and recruits the prokaryotic tubulin homolog TubZ to effect DNA partition. Proc Natl Acad. Sci. USA, 107, 11763-11768.
8. Tang, M., Bideshi, D.K., Park, H.W. and Federici, BA. (2007) Iteron-binding ORF157 and FtsZ-like ORF156 proteins encoded by pBtoxis play a role in its replication in Bacillus thuringiensis subsp. israelensis. J. Bacteriol., 189, 8053-8058. (Pubitemid 350178916)
9. Larsen, RA., Cusumano, C., Fujioka, A., Lim-Fong, G., Patterson, P. and Pogliano, J. (2007) Treadmilling of a prokaryotic tubulin-like protein, TubZ, required for plasmid stability in Bacillus thuringiensis. Genes Dev., 21, 1340-1352. (Pubitemid 46871038)
10. Tinsley, E. and Khan, SA. (2006) A novel FtsZ-like protein is involved in replication of the anthrax toxin-encoding pXO1 plasmid in Bacillus anthracis. J. Bacteriol., 188, 2829-2835.
11. Anand, S.P., Akhtar, P., Tinsley, E., Watkins, S.C. and Khan, SA. (2008) GTP-dependent polymerization of the tubulin-like RepX replication protein encoded by the pXO1 plasmid of Bacillus anthracis. Mol. Microbiol., 67, 881-890. (Pubitemid 351143694)
12. Schumacher, MA. and Funnell, BE. (2005) Structures of ParB bound to DNA reveal mechanism of partition complex formation. Nature, 438, 516-519. (Pubitemid 41742025)
13. Leonard, TA., Butler, P.J. and Lowe, J. (2004) Structural analysis of the chromosome segregation protein Spo0J from Thermus thermophilus. Mol. Microbiol., 53, 419-432. (Pubitemid 38998165)
14. Khare, D., Ziegelin, G., Lanka, E. and Heinemann, U. (2004) Sequence-specific DNA binding determined by contacts outside the helix-turn-helix motif of the ParB homolog KorB. Nat. Struct. Mol. Biol., 11, 656-663. (Pubitemid 38823533)
15. Murayama, K., Orth, P., de la Hoz, A.B., Alonso, J.C. and Saenger, W. (2001) Crystal structure of omega transcriptional repressor encoded by Streptococcus pyogenes plasmid pSM19035 at 1.5 A resolution. J. Mol. Biol., 314, 789-796. (Pubitemid 34087847)
16. Golovanov, A.P., Barilla, D., Golovanova, M., Hayes, F. and Lian, L.Y. (2003) ParG, a protein required for active partition of bacterial plasmids, has a dimeric ribbon-helix-helix structure. Mol. Microbiol., 50, 1141 1153. (Pubitemid 37475849)
17. Weihofen, WA., Cicek, A., Pratto, F., Alonso, J.C. and Saenger, W. (2006) Structures of omega repressors bound to direct and inverted DNA repeats explain modulation of transcription. Nucleic Acids Res., 34, 1450-1458.
18. Schumacher, MA., Glover, T.C., Brzoska, A.J., Jensen, S.O., Dunham, T.D., Skurray, RA. and Firth, N. (2007) Segrosome structure revealed by a complex of ParR with centromere DNA. Nature, 450, 1268-1271.
19. Moller-Jensen, J., Ringgaard, S., Mercogliano, C.P., Gerdes, K. and Lowe, J. (2007) Structural analysis of the ParR/parC plasmid partition complex. EMBO J., 26, 4413-4422. (Pubitemid 47587665)
20. Li, T.Y., Yin, P., Zhou, Y., Zhang, Y., Zhang, Y.Y. and Chen, TA. (2004) Characterization of the replicon of a 51-kb native plasmid from the gram-positive bacterium Leifsonia xyli subsp. cynodontis. FEMS Microbiol. Lett., 236, 33-39. (Pubitemid 38798476)
21. Yin, P., Li, T.Y., Xie, M.H., Jiang, L. and Zhang, Y. (2006) A Type Ib ParB protein involved in plasmid partitioning in a gram-positive bacterium. J. Bacteriol., 188, 8103-8108. (Pubitemid 44845680)
22. Dong, A., Xu, X., Edwards, A.M., Chang, C., Chruszcz, M., Cuff, M., Cymborowski, M., Di Leo, R., Egorova, O., Evdokimova, E. et al. (2007) In situ proteolysis for protein crystallization and structure determination. Nat. Methods, 4, 1019-1021. (Pubitemid 350201773)
23. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326. (Pubitemid 27085611)
24. Sheldrick, GM. (2008) A short history of SHELX. Acta Crystallogr. A, 64, 112-122.
25. Vonrhein, C., Blanc, E., Roversi, P. and Bricogne, G (2007) Automated structure solution with autoSHARP. Methods Mol. Biol., 364, 215-230. (Pubitemid 350183137)
26. Langer, G., Cohen, S.X., Lamzin, V.S. and Perrakis, A. (2008) Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat. Protoc., 3, 1171-1179.
27. Emsley, P. and Cowtan, K. (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr., 60, 2126-2132. (Pubitemid 41742764)
28. Murshudov, G.N., Vagin, A.A., Lebedev, A., Wilson, K.S. and Dodson, E.J. (1999) Efficient anisotropic refinement of macromolecular structures using FFT. Acta Crystallogr. D Biol. Crystallogr., 55, 247-255. (Pubitemid 29053823)
29. Jain, S.S. and Tullius, T.D. (2008) Footprinting protein-DNA complexes using the hydroxyl radical. Nat. Protoc., 3, 1092-1100. (Pubitemid 351818696)
30. Laederach, A., Das, R., Vicens, Q., Pearlman, S.M., Brenowitz, M., Herschlag, D. and Altman, R.B. (2008) Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Nat. Protoc., 3, 1395-1401.
31. Senear, D.F. and Brenowitz, M. (1991) Determination of binding constants for cooperative site-specific protein-DNA interactions using the gel mobility-shift assay. J. Biol. Chem., 266, 13661-13671. (Pubitemid 21907402)
32. Schreiter, E.R. and Drennan, C.L. (2007) Ribbon-helix-helix transcription factors: variations on a theme. Nat. Rev. Microbiol., 5, 710-720. (Pubitemid 47278864)
33. Somers, W.S. and Phillips, S.E. (1992) Crystal structure of the met repressor-operator complex at 2.8 A resolution reveals DNA recognition by beta-strands. Nature, 359, 387-393.
34. Raumann, B.E., Rould, MA., Pabo, C.O. and Sauer, R.T. (1994) DNA recognition by beta-sheets in the Arc repressor-operator crystal structure. Nature, 367, 754-757.
35. Schreiter, E.R., Wang, S.C., Zamble, D.B. and Drennan, C.L. (2006) NikR-operator complex structure and the mechanism of repressor activation by metal ions. Proc Natl Acad. Sci. USA, 103, 13676-13681. (Pubitemid 44413966)
36. Mattison, K., Wilbur, J.S., So, M. and Brennan, R.G. (2006) Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin-antitoxin heterodimers containing pin domains and ribbon-helix-helix motifs. J. Biol. Chem., 281, 37942-37951. (Pubitemid 46042098)
37. Zhou, Y., Larson, J.D., Bottoms, CA., Arturo, E.C., Henzl, M.T., Jenkins, J.L., Nix, J.C., Becker, D.F. and Tanner, J.J. (2008) Structural basis of the transcriptional regulation of the proline utilization regulon by multifunctional PutA. J. Mol. Biol., 381, 174-188.
38. Ni, L., Jensen, S.O., Ky Tonthat, N., Berg, T., Kwong, S.M., Guan, F.H., Brown, M.H., Skurray, RA., Firth, N. and Schumacher, MA. (2009) The Staphylococcus aureus pSK41 plasmid-encoded ArtA protein is a master regulator of plasmid transmission genes and contains a RHH motif used in alternate DNA-binding modes. Nucleic Acids Res., 37, 6970-6983.
39. Gomis-Ruth, F.X., Sola, M., Acebo, P., Parraga, A., Guasch, A., Eritja, R., Gonzalez, A., Espinosa, M., del Solar, G and Coll, M. (1998) The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator. EMBO J., 17, 7404-7415. (Pubitemid 29002708)
40. Cole, C., Barber, J.D. and Barton, GJ. (2008) The Jpred 3 secondary structure prediction server. Nucleic Acids Res., 36, W197-W201.
41. Barilla, D., Carmelo, E. and Hayes, F. (2007) The tail of the ParG DNA segregation protein remodels ParF polymers and enhances ATP hydrolysis via an arginine finger-like motif Proc Natl Acad. Sci. USA, 104, 1811-1816. (Pubitemid 46239861)
42. Carmelo, E., Barilla, D., Golovanov, A.P., Lian, L.Y., Derome, A. and Hayes, F. (2005) The unstructured N-terminal tail of ParG modulates assembly of a quaternary nucleoprotein complex in transcription repression. J. Biol. Chem., 280, 28683-28691. (Pubitemid 41105769)
43. Pratto, F., Cicek, A., Weihofen, WA., Lurz, R., Saenger, W. and Alonso, J.C. (2008) Streptococcus pyogenes pSM19035 requires dynamic assembly of ATP-bound ParA and ParB on parS DNA during plasmid segregation. Nucleic Acids Res., 36, 3676-3689. (Pubitemid 351917530)
44. Brown, B.M. and Sauer, R.T. (1993) Assembly of the Arc repressor-operator complex: cooperative interactions between DNA-bound dimers. Biochemistry, 32, 1354-1363. (Pubitemid 23070661)
45. De La Hoz, A.B., Pratto, F., Misselwitz, R., Speck, C., Weihofen, W., Welfle, K., Saenger, W., Welfle, H. and Alonso, J.C. (2004) Recognition of DNA by omega protein from the broad-host range Streptococcus pyogenes plasmid pSM19035: analysis of binding to operator DNA with one to four heptad repeats. Nucleic Acids Res., 32, 3136-3147. (Pubitemid 39023005)