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| - | [[Image:206d.gif|left|200px]] | |
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| - | {{Structure
| + | ==BASE-PAIR OPENING AND SPERMINE BINDING-B-DNA FEATURES DISPLAYED IN THE CRYSTAL STRUCTURE OF A GAL OPERON FRAGMENT: IMPLICATIONS FOR PROTEIN-DNA RECOGNITION== |
| - | |PDB= 206d |SIZE=350|CAPTION= <scene name='initialview01'>206d</scene>, resolution 2.500Å
| + | <StructureSection load='206d' size='340' side='right'caption='[[206d]], [[Resolution|resolution]] 2.50Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene>
| + | <table><tr><td colspan='2'>[[206d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=206D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=206D FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=206d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=206d OCA], [https://pdbe.org/206d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=206d RCSB], [https://www.ebi.ac.uk/pdbsum/206d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=206d ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=206d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=206d OCA], [http://www.ebi.ac.uk/pdbsum/206d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=206d RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''BASE-PAIR OPENING AND SPERMINE BINDING-B-DNA FEATURES DISPLAYED IN THE CRYSTAL STRUCTURE OF A GAL OPERON FRAGMENT: IMPLICATIONS FOR PROTEIN-DNA RECOGNITION'''
| + | [[Category: Secco AS]] |
| - | | + | [[Category: Tari LW]] |
| - | | + | |
| - | ==Overview==
| + | |
| - | A sequence that is represented frequently in functionally important sites involving protein-DNA interactions is GTG/CAC, suggesting that the trimer may play a role in regulatory processes. The 2.5 A resolution structure of d(CGGTGG)/d(CCACCG), a part of the interior operator (OI, nucleotides +44 to +49) of the gal operon, co-crystallized with spermine, is described herein. The crystal packing arrangement in this structure is unprecedented in a crystal of B-DNA, revealing a close packing of columns of stacked DNA resembling a 5-stranded twisted wire cable. The final structure contains one hexamer duplex, 17 water molecules and 1.5 spermine molecules per crystallographic asymmetric unit. The hexamer exhibits base-pair opening and shearing at T.A resulting in a novel non-Watson-Crick hydrogen-bonding scheme between adenine and thymine in the GTG region. The ability of this sequence to adopt unusual conformations in its GTG region may be a critical factor conferring sequence selectivity on the binding of Gal repressor. In addition, this is the first conclusive example of a crystal structure of spermine with native B-DNA, providing insight into the mechanics of polyamine-DNA binding, as well as possible explanations for the biological action of spermine.
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| - | ==About this Structure==
| + | |
| - | 206D is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=206D OCA].
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| - | | + | |
| - | ==Reference==
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| - | Base-pair opening and spermine binding--B-DNA features displayed in the crystal structure of a gal operon fragment: implications for protein-DNA recognition., Tari LW, Secco AS, Nucleic Acids Res. 1995 Jun 11;23(11):2065-73. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7596838 7596838]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Secco, A S.]] | + | |
| - | [[Category: Tari, L W.]] | + | |
| - | [[Category: b-dna]]
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| - | [[Category: double helix]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:44:01 2008''
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