||Saci_0101 is commonly believed to be a histone-like protein involved in genomic DNA compaction from Sulfolobus acidocaldarius. Here, to obtain a detailed understanding of its architectural properties, we present two crystal structures of wild type Saci_0101 in different crystal forms at 1.30 Å and 1.40 Å resolution, respectively. The overall crystal structures of both wild type are similar with the homologues of Sso7c4 in S. solfataricus and have a homodimeric DNA-binding fold forming a swapped -loop- ‘Ying-Yang’ topology. The crystal structure of its single mutant, I20M also has been solved at 1.55 Å resolution. Interestingly, the single mutation by replacing Ile with Met leads to the shortening of 1 helix and even makes the mutant structure much more static than the wild type, proved by the very small B-factor of 14 in I20M structure. In fluorescence polarization study, wild type Saci_0101 binds to a 20-bp double-stranded DNA with a binding affinity of 1.23 ± 0.19 M, which is close to other nonspecific dsDNA-binding proteins in Sulfolobus species. The EM studies show Saci_0101 may shape DNA as a wrapper and a briddger, which suggests Saci_0101 play a role in DNA packaging and duplex stabilization at the elevated growth temperatures.|
||1. Q. She et al., The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci U S A 98, 7835-7840 (2001).|
2. L. Chen et al., The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota. J Bacteriol 187, 4992-4999 (2005).
3. Y. G. Gao et al., The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA. Nat Struct Biol 5, 782-786 (1998).
4. P. Agback, H. Baumann, S. Knapp, R. Ladenstein, T. Hard, Architecture of nonspecific protein-DNA interactions in the Sso7d-DNA complex. Nat Struct Biol 5, 579-584 (1998).
5. B. N. Wardleworth, R. J. Russell, S. D. Bell, G. L. Taylor, M. F. White, Structure of Alba: an archaeal chromatin protein modulated by acetylation. EMBO J 21, 4654-4662 (2002).
6. C. H. Hsu, A. H. Wang, The DNA-recognition fold of Sso7c4 suggests a new member of SpoVT-AbrB superfamily from archaea. Nucleic Acids Res 39, 6764-6774 (2011).
7. M. S. Luijsterburg, M. F. White, R. van Driel, R. T. Dame, The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes. Crit Rev Biochem Mol Biol 43, 393-418 (2008).
8. K. Nightingale, S. Dimitrov, R. Reeves, A. P. Wolffe, Evidence for a shared structural role for HMG1 and linker histones B4 and H1 in organizing chromatin. EMBO J 15, 548-561 (1996).
9. K. K. Swinger, P. A. Rice, IHF and HU: flexible architects of bent DNA. Curr Opin Struct Biol 14, 28-35 (2004).
10. R. Schneider et al., An architectural role of the Escherichia coli chromatin protein FIS in organising DNA. Nucleic Acids Res 29, 5107-5114 (2001).
11. S. Rimsky, Structure of the histone-like protein H-NS and its role in regulation and genome superstructure. Curr Opin Microbiol 7, 109-114 (2004).
12. Z. Otwinowski, W. Minor, Processing of X-ray diffraction data collected in oscillation mode. Method Enzymol 276, 307-326 (1997).
13. M. D. Winn et al., Overview of the CCP4 suite and current developments. Acta Crystallogr D 67, 235-242 (2011).
14. G. Langer, S. X. Cohen, V. S. Lamzin, A. Perrakis, Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc 3, 1171-1179 (2008).
15. P. Emsley, B. Lohkamp, W. G. Scott, K. Cowtan, Features and development of Coot. Acta Crystallogr D 66, 486-501 (2010).
16. G. N. Murshudov et al., REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr 67, 355-367 (2011).
17. A. M. Rossi, C. W. Taylor, Analysis of protein-ligand interactions by fluorescence polarization. Nat Protoc 6, 365-387 (2011).
18. J. D. Griffith, G. Christiansen, Electron microscope visualization of chromatin and other DNA-protein complexes. Annu Rev Biophys Bioeng 7, 19-35 (1978).
19. S. M. Hartig, Basic image analysis and manipulation in ImageJ. Curr Protoc Mol Biol Chapter 14, Unit14 15 (2013).