307d
From Proteopedia
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|PDB= 307d |SIZE=350|CAPTION= <scene name='initialview01'>307d</scene>, resolution 1.850Å | |PDB= 307d |SIZE=350|CAPTION= <scene name='initialview01'>307d</scene>, resolution 1.850Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |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> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |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> | ||
}} | }} | ||
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[[Category: double helix]] | [[Category: double helix]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:21:07 2008'' |
Revision as of 02:21, 31 March 2008
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| , resolution 1.850Å | |||||||
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| Ligands: | , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
STRUCTURE OF A DNA ANALOG OF THE PRIMER FOR HIV-1 RT SECOND STRAND SYNTHESIS
Overview
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.
About this Structure
307D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
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:9223643
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