1ekd

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[[Image:1ekd.gif|left|200px]]
[[Image:1ekd.gif|left|200px]]
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{{Structure
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|PDB= 1ekd |SIZE=350|CAPTION= <scene name='initialview01'>1ekd</scene>
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The line below this paragraph, containing "STRUCTURE_1ekd", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
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{{STRUCTURE_1ekd| PDB=1ekd | SCENE= }}
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|RELATEDENTRY=
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ekd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ekd OCA], [http://www.ebi.ac.uk/pdbsum/1ekd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ekd RCSB]</span>
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'''NMR AND MOLECULAR MODELING REVEAL THAT DIFFERENT HYDROGEN BONDING PATTERNS ARE POSSIBLE FOR GU PAIRS: ONE HYDROGEN BOND FOR EACH GU PAIR IN R(GGCGUGCC)2 AND TWO FOR EACH GU PAIR IN R(GAGUGCUC)2'''
'''NMR AND MOLECULAR MODELING REVEAL THAT DIFFERENT HYDROGEN BONDING PATTERNS ARE POSSIBLE FOR GU PAIRS: ONE HYDROGEN BOND FOR EACH GU PAIR IN R(GGCGUGCC)2 AND TWO FOR EACH GU PAIR IN R(GAGUGCUC)2'''
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==About this Structure==
==About this Structure==
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1EKD 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=1EKD OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EKD OCA].
==Reference==
==Reference==
Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G.U pairs: one hydrogen bond for each G.U pair in r(GGCGUGCC)(2) and two for each G.U pair in r(GAGUGCUC)(2)., Chen X, McDowell JA, Kierzek R, Krugh TR, Turner DH, Biochemistry. 2000 Aug 1;39(30):8970-82. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10913310 10913310]
Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G.U pairs: one hydrogen bond for each G.U pair in r(GGCGUGCC)(2) and two for each G.U pair in r(GAGUGCUC)(2)., Chen X, McDowell JA, Kierzek R, Krugh TR, Turner DH, Biochemistry. 2000 Aug 1;39(30):8970-82. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10913310 10913310]
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[[Category: Protein complex]]
 
[[Category: Chen, X.]]
[[Category: Chen, X.]]
[[Category: Kierzek, R.]]
[[Category: Kierzek, R.]]
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[[Category: McDowell, J A.]]
[[Category: McDowell, J A.]]
[[Category: Turner, D H.]]
[[Category: Turner, D H.]]
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[[Category: double helix]]
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[[Category: Double helix]]
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[[Category: gu pair]]
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[[Category: Gu pair]]
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[[Category: hydrogen bond]]
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[[Category: Hydrogen bond]]
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[[Category: rna]]
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[[Category: Rna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 15:12:27 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:04:27 2008''
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Revision as of 12:12, 2 May 2008

Image:1ekd.gif

Template:STRUCTURE 1ekd

NMR AND MOLECULAR MODELING REVEAL THAT DIFFERENT HYDROGEN BONDING PATTERNS ARE POSSIBLE FOR GU PAIRS: ONE HYDROGEN BOND FOR EACH GU PAIR IN R(GGCGUGCC)2 AND TWO FOR EACH GU PAIR IN R(GAGUGCUC)2


Overview

G.U pairs occur frequently and have many important biological functions. The stability of symmetric tandem G.U motifs depends both on the adjacent Watson-Crick base pairs, e.g., 5'G > 5'C, and the sequence of the G.U pairs, i.e., 5'-UG-3' > 5'-GU-3', where an underline represents a nucleotide in a G.U pair [Wu, M., McDowell, J. A., and Turner, D. H. (1995) Biochemistry 34, 3204-3211]. In particular, at 37 degrees C, the motif 5'-CGUG-3' is less stable by approximately 3 kcal/mol compared with other symmetric tandem G.U motifs with G-C as adjacent pairs: 5'-GGUC-3', 5'-GUGC-3', and 5'-CUGG-3'. The solution structures of r(GAGUGCUC)(2) and r(GGCGUGCC)(2) duplexes have been determined by NMR and restrained simulated annealing. The global geometry of both duplexes is close to A-form, with some distortions localized in the tandem G.U pair region. The striking discovery is that in r(GGCGUGCC)(2) each G.U pair apparently has only one hydrogen bond instead of the two expected for a canonical wobble pair. In the one-hydrogen-bond model, the distance between GO6 and UH3 is too far to form a hydrogen bond. In addition, the temperature dependence of the imino proton resonances is also consistent with the different number of hydrogen bonds in the G.U pair. To test the NMR models, U or G in various G.U pairs were individually replaced by N3-methyluridine or isoguanosine, respectively, thus eliminating the possibility of hydrogen bonding between GO6 and UH3. The results of thermal melting studies on duplexes with these substitutions support the NMR models.

About this Structure

Full crystallographic information is available from OCA.

Reference

Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G.U pairs: one hydrogen bond for each G.U pair in r(GGCGUGCC)(2) and two for each G.U pair in r(GAGUGCUC)(2)., Chen X, McDowell JA, Kierzek R, Krugh TR, Turner DH, Biochemistry. 2000 Aug 1;39(30):8970-82. PMID:10913310 Page seeded by OCA on Fri May 2 15:12:27 2008

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