1q2t
From Proteopedia
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|PDB= 1q2t |SIZE=350|CAPTION= <scene name='initialview01'>1q2t</scene> | |PDB= 1q2t |SIZE=350|CAPTION= <scene name='initialview01'>1q2t</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=5CM:5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1rme|1RME]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q2t OCA], [http://www.ebi.ac.uk/pdbsum/1q2t PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1q2t RCSB]</span> | ||
}} | }} | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Leroy, J L.]] | [[Category: Leroy, J L.]] | ||
| - | [[Category: dna solution structure | + | [[Category: dna solution structure]] |
| + | [[Category: hemiprotonated base-pair]] | ||
| + | [[Category: i-motif]] | ||
| + | [[Category: protonated cytidine]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:08:03 2008'' |
Revision as of 20:08, 30 March 2008
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| Ligands: | , , | ||||||
| Related: | 1RME
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Solution structure of d(5mCCTCTCC)4
Overview
The i-motif is a four-stranded structure built by intercalation in head-to-tail orientation of two parallel duplexes associated by hemi-protonated C.C(+) pairs. Using NMR methods, we investigated the structure, the base-pair opening kinetics and the internal motions of three i-motif tetramers: [d(5mCCTCnTCC)](4) (n=1, 2, 3). These tetramers cannot accommodate the intercalation of two T.T pairs in face-to-face orientation. They are built by intercalation of two symmetrical duplexes whose contacting T3/TM thymidine bases (M=5, 6, 7) are either base-paired or unstacked. The arrangement of the unstacked/paired thymidine bases of the two T/T groups results in the formation of two different conformations. One, fully symmetric, whose thymidine bases T3 and TM are unstacked and base-paired respectively. The other is the asymmetric assembly of two duplexes: one where both thymidine bases are unstacked and the other with two T.T pairs. The proportion of the symmetric conformer increases from a value beyond the detection threshold for n=1, to 19% for n=2 and up to more than 95% for n=3. The exchange cross-peaks connecting together the intercalated duplexes of [d(5mCCTCTCC)](4) and [d(5mCCTCCTCC)](4) reveal a structural interconversion induced by the simultaneous opening/closing of the contacting T3/TM thymidine bases. In [d(5mCCTCCTCC)](4) the motion of the T3/T6 groups triggers the interconversion of the symmetric and asymmetric conformations. In [d(5mCCTCTCC)](4) the intercalated duplexes exchange their structures in an apparently concerted motion, suggesting the simultaneous opening/closing of two distant T3/T5* and T5/T3* switching groups. The spectrum of [d(5mCCTCCCTCC)](4) is fully symmetric and, for this reason, its spectrum gives no indication for duplex interconversion. Nevertheless, the imino proton exchange kinetics argues for a switching motion of the T3/T7 group. Duplex interconversion is not detectable in that case, due to the tetramer symmetry. The origin of the structural conflict hindering the intercalation of two T.T pairs into the i-motif is discussed.
About this Structure
1Q2T is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
T.T pair intercalation and duplex interconversion within i-motif tetramers., Leroy JL, J Mol Biol. 2003 Oct 10;333(1):125-39. PMID:14516748
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