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| - | [[Image:307d.gif|left|200px]] | |
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| - | {{Structure
| + | ==Structure of a DNA analog of the primer for HIV-1 RT second strand synthesis== |
| - | |PDB= 307d |SIZE=350|CAPTION= <scene name='initialview01'>307d</scene>, resolution 1.850Å
| + | <StructureSection load='307d' size='340' side='right'caption='[[307d]], [[Resolution|resolution]] 1.85Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <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>
| + | <table><tr><td colspan='2'>[[307d]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=307D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=307D 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]] 1.85Å</td></tr> |
| - | |GENE=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=307d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=307d OCA], [https://pdbe.org/307d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=307d RCSB], [https://www.ebi.ac.uk/pdbsum/307d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=307d ProSAT]</span></td></tr> |
| - | |DOMAIN=
| + | </table> |
| - | |RELATEDENTRY=
| + | __TOC__ |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=307d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=307d OCA], [http://www.ebi.ac.uk/pdbsum/307d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=307d RCSB]</span>
| + | </StructureSection> |
| - | }}
| + | [[Category: Large Structures]] |
| - | | + | [[Category: Cascio D]] |
| - | '''STRUCTURE OF A DNA ANALOG OF THE PRIMER FOR HIV-1 RT SECOND STRAND SYNTHESIS'''
| + | [[Category: Dickerson RE]] |
| - | | + | [[Category: Grzeskowiak K]] |
| - | | + | [[Category: Han GW]] |
| - | ==Overview==
| + | [[Category: Kopka ML]] |
| - | The non-self-complementary DNA decamer C-A-A-A-G-A-A-A-A-G/C-T-T-T-T-C-T-T-T-G is a DNA/DNA analogue of a portion of the polypurine tract or PPT, which is a RNA/DNA hybrid that serves as a primer for synthesis of the (+) DNA strand by HIV reverse transcriptase (RT), and which is not digested by the RNase H domain of reverse transcriptase following (-) strand synthesis. The same unusual conformation that eludes RNase H, thought to be a change in width of minor groove, may also be responsible for the inhibition of HIV RT by minor groove binding drugs such as distamycin and their bis-linked derivatives. The present X-ray crystal structure of this DNA decamer exhibits the usual properties of A-tract B-DNA under biologically relevant conditions: large propeller twist of base-pairs, narrowed minor groove, and a straight helix axis. Groove narrowing is fully developed in the A-A-A-A region, but not in the A-A-A region, which previous investigators have proposed as being too short to exhibit typical A-tract properties. The RNA/DNA hybrid produced by HIV reverse transcriptase during (-) strand synthesis presumably forms a "heteromerous" or H-helix with narrower minor groove than an A-helical RNA/RNA duplex. If the narrowing of minor groove in A-tract H-helices is comparable to that seen in A-tract B-helices, then the narrowed minor groove of the polypurine tract could make the second primer site both (1) impervious to RNase H digestion, and (2) susceptible to inhibition by minor groove binding drugs.
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| - | ==About this Structure==
| + | |
| - | 307D 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=307D OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Structure of a DNA analog of the primer for HIV-1 RT second strand synthesis., Han GW, Kopka ML, Cascio D, Grzeskowiak K, Dickerson RE, J Mol Biol. 1997 Jun 27;269(5):811-26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9223643 9223643]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Cascio, D.]] | + | |
| - | [[Category: Dickerson, R E.]] | + | |
| - | [[Category: Grzeskowiak, K.]] | + | |
| - | [[Category: Han, G W.]] | + | |
| - | [[Category: Kopka, M L.]] | + | |
| - | [[Category: b-dna]]
| + | |
| - | [[Category: double helix]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:21:07 2008''
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