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| | ==Crystal structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers== | | ==Crystal structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers== |
| - | <StructureSection load='1wd1' size='340' side='right' caption='[[1wd1]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='1wd1' size='340' side='right'caption='[[1wd1]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1wd1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33909 Atcc 33909]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WD1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WD1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1wd1]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius Sulfolobus acidocaldarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WD1 FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1azp|1azp]], [[1wd0|1wd0]]</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wd1 OCA], [http://pdbe.org/1wd1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wd1 RCSB], [http://www.ebi.ac.uk/pdbsum/1wd1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wd1 ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wd1 OCA], [https://pdbe.org/1wd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wd1 RCSB], [https://www.ebi.ac.uk/pdbsum/1wd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wd1 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DN71_SULAC DN71_SULAC]] Constrain negative DNA supercoils; may be involved in maintaining the integrity of their genome at high temperature. | + | [https://www.uniprot.org/uniprot/DN7D_SULAC DN7D_SULAC] Can constrain negative DNA supercoils. May be involved in maintaining the integrity of the genome at high temperature.[UniProtKB:P61990] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 33909]] | + | [[Category: Large Structures]] |
| - | [[Category: Chen, C Y]] | + | [[Category: Sulfolobus acidocaldarius]] |
| - | [[Category: Chou, C C]] | + | [[Category: Chen C-Y]] |
| - | [[Category: Chu, H M]] | + | [[Category: Chou C-C]] |
| - | [[Category: Ko, T P]] | + | [[Category: Chu H-M]] |
| - | [[Category: Wang, A H.J]] | + | [[Category: Ko T-P]] |
| - | [[Category: Protein-dna complex]]
| + | [[Category: Wang AH-J]] |
| - | [[Category: Structural protein-dna complex]]
| + | |
| Structural highlights
Function
DN7D_SULAC Can constrain negative DNA supercoils. May be involved in maintaining the integrity of the genome at high temperature.[UniProtKB:P61990]
Publication Abstract from PubMed
The protein Sac7d belongs to a class of small chromosomal proteins from the hyperthermophilic archaeon Sulfolobus acidocaldarius. Two new crystal forms of Sac7d in complex with the DNA decamers CCTATATAGG and CCTACGTAGG were obtained and their structures were determined by molecular replacement. The refined models yielded R/Rfree values of 0.221/0.257 and 0.248/0.290 at 1.9 and 2.2 A resolution, respectively. The protein structures are similar to the previously determined structure of Sac7d-GCGATCGC (PDB code 1azp), but the DNA molecules are more bent overall, by 14-20 degrees. The relative positions of the Sac7d protein and the bound DNA also differ by rotations of 6-10 degrees and translations of 1.0-2.4 A. In addition to the water molecules in the central cavity, three additional conserved water molecules are found that mediate the protein-DNA interactions. The decamer DNA fragments form virtual double helices in the crystal, with a unit length of eight base pairs. The molecular packing of the new crystal forms differs from that of 1azp. The terminal nucleotides are opened up and form triple base pairs with other DNA molecules. Through lattice contacts, the Sac7d molecule also makes additional interactions with DNA, whereas only limited protein-protein interactions are seen.
Structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers.,Ko TP, Chu HM, Chen CY, Chou CC, Wang AH Acta Crystallogr D Biol Crystallogr. 2004 Aug;60(Pt 8):1381-7. Epub 2004, Jul 21. PMID:15272160[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ko TP, Chu HM, Chen CY, Chou CC, Wang AH. Structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers. Acta Crystallogr D Biol Crystallogr. 2004 Aug;60(Pt 8):1381-7. Epub 2004, Jul 21. PMID:15272160 doi:http://dx.doi.org/10.1107/S0907444904012065
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