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[[Image:229d.gif|left|200px]]


{{Structure
==DNA ANALOG OF YEAST TRANSFER RNA PHE ANTICODON DOMAIN WITH MODIFIED BASES 5-METHYL CYTOSINE AND 1-METHYL GUANINE==
|PDB= 229d |SIZE=350|CAPTION= <scene name='initialview01'>229d</scene>
<StructureSection load='229d' size='340' side='right'caption='[[229d]]' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=5CM:5-METHYL-2&#39;-DEOXY-CYTIDINE-5&#39;-MONOPHOSPHATE'>5CM</scene>, <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=MG1:2&#39;-DEOXY-1-METHYLGUANOSINE+5&#39;-(DIHYDROGEN+PHOSPHATE)'>MG1</scene>, <scene name='pdbligand=UMP:2&#39;-DEOXYURIDINE+5&#39;-MONOPHOSPHATE'>UMP</scene>
<table><tr><td colspan='2'>[[229d]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=229D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=229D FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=MG1:2-DEOXY-1-METHYLGUANOSINE+5-(DIHYDROGEN+PHOSPHATE)'>MG1</scene>, <scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</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=229d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=229d OCA], [https://pdbe.org/229d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=229d RCSB], [https://www.ebi.ac.uk/pdbsum/229d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=229d ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=229d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=229d OCA], [http://www.ebi.ac.uk/pdbsum/229d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=229d RCSB]</span>
<div style="background-color:#fffaf0;">
}}
== Publication Abstract from PubMed ==
 
'''DNA ANALOG OF YEAST TRANSFER RNA PHE ANTICODON DOMAIN WITH MODIFIED BASES 5-METHYL CYTOSINE AND 1-METHYL GUANINE'''
 
 
==Overview==
Design of biologically active DNA analogues of the yeast tRNA(Phe) anticodon domain, tDNAPheAC, required the introduction of a d(m5C)-dependent, Mg(2+)-induced structural transition and the d(m1G) disruption of an intra-loop dC.dG base pair. The modifications were introduced at residues corresponding to m5C-40 and wybutosine-37 in tRNA(Phe). Modified tDNAPheAC inhibited translation by 50% at a tDNAPheAC:ribosome ratio of 8:1. The molecule's structure has been determined by NMR spectroscopy and restrained molecular dynamics with an overall r.m.s.d. of 2.8 A and 1.7 A in the stem, and is similar to the tRNA(Phe) anticodon domain in conformation and dimensions. The tDNAPheAC structure may provide a guide for the design of translation inhibitors as potential therapeutic agents.
Design of biologically active DNA analogues of the yeast tRNA(Phe) anticodon domain, tDNAPheAC, required the introduction of a d(m5C)-dependent, Mg(2+)-induced structural transition and the d(m1G) disruption of an intra-loop dC.dG base pair. The modifications were introduced at residues corresponding to m5C-40 and wybutosine-37 in tRNA(Phe). Modified tDNAPheAC inhibited translation by 50% at a tDNAPheAC:ribosome ratio of 8:1. The molecule's structure has been determined by NMR spectroscopy and restrained molecular dynamics with an overall r.m.s.d. of 2.8 A and 1.7 A in the stem, and is similar to the tRNA(Phe) anticodon domain in conformation and dimensions. The tDNAPheAC structure may provide a guide for the design of translation inhibitors as potential therapeutic agents.


==About this Structure==
Design, biological activity and NMR-solution structure of a DNA analogue of yeast tRNA(Phe) anticodon domain.,Basti MM, Stuart JW, Lam AT, Guenther R, Agris PF Nat Struct Biol. 1996 Jan;3(1):38-44. PMID:8548453<ref>PMID:8548453</ref>
229D 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=229D OCA].
 
==Reference==
Design, biological activity and NMR-solution structure of a DNA analogue of yeast tRNA(Phe) anticodon domain., Basti MM, Stuart JW, Lam AT, Guenther R, Agris PF, Nat Struct Biol. 1996 Jan;3(1):38-44. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8548453 8548453]
[[Category: Protein complex]]
[[Category: Agris, P F.]]
[[Category: Basti, M M.]]
[[Category: Guenther, R.]]
[[Category: Lam, A T.]]
[[Category: Stuart, J W.]]
[[Category: anticodon]]
[[Category: dna]]
[[Category: hairpin loop]]
[[Category: transfer rna]]


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:44:43 2008''
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 229d" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Agris PF]]
[[Category: Basti MM]]
[[Category: Guenther R]]
[[Category: Lam AT]]
[[Category: Stuart JW]]

Latest revision as of 16:31, 13 December 2023

DNA ANALOG OF YEAST TRANSFER RNA PHE ANTICODON DOMAIN WITH MODIFIED BASES 5-METHYL CYTOSINE AND 1-METHYL GUANINE

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