2awv
From Proteopedia
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|PDB= 2awv |SIZE=350|CAPTION= <scene name='initialview01'>2awv</scene> | |PDB= 2awv |SIZE=350|CAPTION= <scene name='initialview01'>2awv</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MCY:5-METHYL-2'-DEOXYCYTIDINE'>MCY</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1q2t|1Q2T]], [[1rme|1RME]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2awv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2awv OCA], [http://www.ebi.ac.uk/pdbsum/2awv PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2awv RCSB]</span> | ||
}} | }} | ||
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[[Category: i-motif]] | [[Category: i-motif]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:58:23 2008'' |
Revision as of 22:58, 30 March 2008
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| Ligands: | , , , | ||||||
| Related: | 1Q2T, 1RME
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
NMR Structural Analysis of the dimer of 5MCCTCATCC
Overview
At slightly acidic pH, the association of two d(5mCCTCACTCC) strands results in the formation of an i-motif dimer. Using NMR methods, we investigated the structure of [d(5mCCTCACTCC)]2, the internal motion of the base pairs stacked in the i-motif core, the dimer formation and dissociation kinetics versus pH. The excellent resolution of the 1H and 31P spectra provided the determination of dihedral angles, which together with a large set of distance restraints, improve substantially the definition of the sugar-phosphate backbone by comparison with previous NMR studies of i-motif structures. [d(5mCCTCACTCC)]2 is built by intercalation of two symmetrical hairpins held together by six symmetrical C*C+ pairs and by pair T7*T7. The hairpin loops that are formed by a single residue, A5, cross the narrow grooves on the same side of the i-motif core. The base pair intercalation order is C9*C9+/5mC1*5mC1+/C8*C8+/C2*C2+/T7.T7/C6*C6+/C4*C4+. The T3 bases are flipped out in the wide grooves. The core of the structure includes four long-lived pairs whose lifetimes at 15 degrees C range from 100 s (C8*C8+) to 0.18 s (T7*T7). The formation rate and the lifetime of [d(5mCCTCACTCC)]2 were measured between pH 6.8 and 4.8. The dimer formation rate is three to four magnitude orders slower than that of a B-DNA duplex. It depends on pH, as it must occur for a bimolecular process involving non cooperative association of neutral and protonated residues. In the range of pH investigated, the dimer lifetime, 500 s at 0 degrees C, pH 6.8, varies approximately as 10(-pH).
About this Structure
2AWV is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure, internal motions and association-dissociation kinetics of the i-motif dimer of d(5mCCTCACTCC)., Canalia M, Leroy JL, Nucleic Acids Res. 2005 Oct 4;33(17):5471-81. Print 2005. PMID:16204453
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