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| - | [[Image:1edr.gif|left|200px]] | |
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| - | {{Structure
| + | ==MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGMO6AATTCGCG) AT 1.6 ANGSTROM== |
| - | |PDB= 1edr |SIZE=350|CAPTION= <scene name='initialview01'>1edr</scene>, resolution 1.60Å
| + | <StructureSection load='1edr' size='340' side='right'caption='[[1edr]], [[Resolution|resolution]] 1.60Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=A47:N6-METHOXY+ADENOSINE+5'-MONOPHOSPHATE'>A47</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene>
| + | <table><tr><td colspan='2'>[[1edr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EDR FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A47:N6-METHOXY+ADENOSINE+5-MONOPHOSPHATE'>A47</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</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=1edr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1edr OCA], [https://pdbe.org/1edr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1edr RCSB], [https://www.ebi.ac.uk/pdbsum/1edr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1edr ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1edr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1edr OCA], [http://www.ebi.ac.uk/pdbsum/1edr PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1edr RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGMO6AATTCGCG) AT 1.6 ANGSTROM'''
| + | [[Category: Chatake T]] |
| - | | + | [[Category: Hikima T]] |
| - | | + | [[Category: Matsuda A]] |
| - | ==Overview==
| + | [[Category: Ono A]] |
| - | In a previous paper, 2'-deoxy-N(6)-methoxyadenosine (mo(6)A) was shown to form a mismatch base-pair with 2'-deoxycytidine with a Watson-Crick-type geometry. To fully understand the structural basis of genetic mutations with damaged DNA, it is necessary to examine whether the methoxylated adenine residue still has the ability to form the regular Watson-Crick pairing with a thymine residue. Therefore, a DNA dodecamer with the sequence d(CGCGmo(6)AATTCGCG) has been synthesized and its crystal structure determined. The methoxylation has no significant effect on the overall DNA conformation, which is that of a standard B-form duplex. The methoxylated adenine moieties adopt the amino tautomer with an anti conformation around the C(6)-N(6) bond to the N(1) atom, and they form a Watson-Crick base-pair with thymine residues on the opposite strand, similar to an unmodified adenine residue. It is concluded that methoxylated adenine can present two alternate faces for base-pairing, thanks to the amino<-->imino tautomerism allowed by methoxylation. Based on this property, two gene transition routes are proposed.
| + | [[Category: Takenaka A]] |
| - | | + | [[Category: Ueno Y]] |
| - | ==About this Structure==
| + | |
| - | 1EDR 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=1EDR OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Crystallographic studies on damaged DNAs. II. N(6)-methoxyadenine can present two alternate faces for Watson-Crick base-pairing, leading to pyrimidine transition mutagenesis., Chatake T, Hikima T, Ono A, Ueno Y, Matsuda A, Takenaka A, J Mol Biol. 1999 Dec 17;294(5):1223-30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10600380 10600380]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Chatake, T.]] | + | |
| - | [[Category: Hikima, T.]] | + | |
| - | [[Category: Matsuda, A.]] | + | |
| - | [[Category: Ono, A.]] | + | |
| - | [[Category: Takenaka, A.]] | + | |
| - | [[Category: Ueno, Y.]] | + | |
| - | [[Category: b-dna]]
| + | |
| - | [[Category: damaged dna]]
| + | |
| - | [[Category: deoxyribonucleic acid]]
| + | |
| - | [[Category: double helix]]
| + | |
| - | [[Category: methoxyadenosine]]
| + | |
| - | [[Category: modified nucleotide]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:00:27 2008''
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