206d: Difference between revisions

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~~[[Image:206d.gif|left|200px]]~~

~~{{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.~~500~~Å

~~|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 guided tour on the structure components use [https://proteopedia.org/fgij/fg.htm?mol=206D FirstGlance].

~~|ACTIVITY~~=

</td></tr><tr id='method'><td class="sblockLbl">[[Empirical_models|Method:]]</td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr>

~~|GENE~~=

<tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr>

~~|DOMAIN=~~

<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[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]</td></tr>

~~|RELATEDENTRY=~~

</table>

~~|RESOURCES~~=[~~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]~~~~

__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.~~

~~==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~~].

~~==Reference==~~

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]~~

[[Category: ~~Protein complex~~]]

[[Category: Secco~~, A S.~~]]

[[Category: Tari~~, L W.]]~~

~~[[Category: b-dna~~]]

~~[[Category: double helix]]~~

~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:44:01 2008''~~

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@@ Line 1: / Line 1: @@
-[[Image:206d.gif|left|200px]]
- {{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 2.500&Aring;
+<StructureSection load='206d' size='340' side='right'caption='[[206d]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-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]] 2.5&#8491;</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.
-==About this Structure==
-D 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].
-==Reference==
-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]
-[[Category: Protein complex]]
-[[Category: Secco, A S.]]
-[[Category: Tari, L W.]]
-[[Category: b-dna]]
-[[Category: double helix]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:44:01 2008''