This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
206d
From Proteopedia
| Line 1: | Line 1: | ||
[[Image:206d.gif|left|200px]] | [[Image:206d.gif|left|200px]] | ||
| - | + | <!-- | |
| - | + | The line below this paragraph, containing "STRUCTURE_206d", creates the "Structure Box" on the page. | |
| - | + | You may change the PDB parameter (which sets the PDB file loaded into the applet) | |
| - | + | or the SCENE parameter (which sets the initial scene displayed when the page is loaded), | |
| - | | | + | or leave the SCENE parameter empty for the default display. |
| - | | | + | --> |
| - | + | {{STRUCTURE_206d| PDB=206d | SCENE= }} | |
| - | + | ||
| - | + | ||
| - | }} | + | |
'''BASE-PAIR OPENING AND SPERMINE BINDING-B-DNA FEATURES DISPLAYED IN THE CRYSTAL STRUCTURE OF A GAL OPERON FRAGMENT: IMPLICATIONS FOR PROTEIN-DNA RECOGNITION''' | '''BASE-PAIR OPENING AND SPERMINE BINDING-B-DNA FEATURES DISPLAYED IN THE CRYSTAL STRUCTURE OF A GAL OPERON FRAGMENT: IMPLICATIONS FOR PROTEIN-DNA RECOGNITION''' | ||
| Line 19: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | + | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=206D OCA]. | |
==Reference== | ==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] | 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: Secco, A S.]] | ||
[[Category: Tari, L W.]] | [[Category: Tari, L W.]] | ||
| - | [[Category: | + | [[Category: B-dna]] |
| - | [[Category: | + | [[Category: Double helix]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 18:17:58 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 15:18, 3 May 2008
BASE-PAIR OPENING AND SPERMINE BINDING-B-DNA FEATURES DISPLAYED IN THE CRYSTAL STRUCTURE OF A GAL OPERON FRAGMENT: IMPLICATIONS FOR PROTEIN-DNA RECOGNITION
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
Full crystallographic information is available from 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:7596838 Page seeded by OCA on Sat May 3 18:17:58 2008
