2lb4: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(One intermediate revision by the same user not shown)
Line 1: Line 1:


==DNA / RNA Hybrid containing a central stereo specific Sp borano phosphate linkage==
==DNA / RNA Hybrid containing a central stereo specific Sp borano phosphate linkage==
<StructureSection load='2lb4' size='340' side='right'caption='[[2lb4]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
<StructureSection load='2lb4' size='340' side='right'caption='[[2lb4]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2lb4]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LB4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2lb4]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LB4 FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGR:[[(2R,3S,5R)-5-(2-AZANYL-6-OXO-1H-PURIN-9-YL)-3-HYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]BORANUIDE'>BGR</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2lar|2lar]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGR:[[(2R,3S,5R)-5-(2-AZANYL-6-OXO-1H-PURIN-9-YL)-3-HYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]BORANUIDE'>BGR</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2lb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lb4 OCA], [https://pdbe.org/2lb4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lb4 RCSB], [https://www.ebi.ac.uk/pdbsum/2lb4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lb4 ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2lb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lb4 OCA], [https://pdbe.org/2lb4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lb4 RCSB], [https://www.ebi.ac.uk/pdbsum/2lb4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lb4 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Numerous DNA chemistries for improving oligodeoxynucleotide (ODN)-based RNA targeting have been explored. The majority of the modifications render the ODN/RNA target insensitive to RNase H1. Borano phosphonate ODN's are among the few modifications that are tolerated by RNase H1. To understand the effect of the stereochemistry of the BH(3) modification on the nucleic acid structure and RNase H1 enzyme activity, we have investigated two DNA/RNA hybrids containing either a R(P) or S(P) BH(3) modification by nuclear magnetic resonance (NMR) spectroscopy. T(M) studies show that the stabilities of R(P) and S(P) modified DNA/RNA hybrids are essentially identical (313.8 K) and similar to that of an unmodified control (312.9 K). The similarity is also reflected in the imino proton spectra. To characterize such similar structures, we used a large number of NMR restraints (including dipolar couplings and backbone torsion angles) to determine structural features that were important for RNase H1 activity. The final NMR structures exhibit excellent agreement with the data (total R(x) values of &lt;6%) with helical properties between those of an A and B helix. Subtle backbone variations are observed in the DNA near the modification, while the RNA strands are relatively unperturbed. In the case of the S(P) modification, for which more perturbations are recorded, a slightly narrower minor groove is also obtained. Unique NOE base contacts localize the S(P) BH(3) group in the major groove while the R(P) BH(3) group points away from the DNA. However, this creates a potential clash of the R(P) BH(3) groups with important RNase H1 residues in a complex, while the S(P) BH(3) groups could be tolerated. We therefore predict that on the basis of our NMR structures a fully R(P) BH(3) DNA/RNA hybrid would not be a substrate for RNase H1.
Structural basis of the RNase H1 activity on stereo regular Borano phosphonate DNA/RNA hybrids.,Johnson CN, Spring AM, Sergueev D, Shaw BR, Germann MW Biochemistry. 2011 May 17;50(19):3903-12. Epub 2011 Apr 19. PMID:21443203<ref>PMID:21443203</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2lb4" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Germann, M W]]
[[Category: Germann MW]]
[[Category: Johnson, C N]]
[[Category: Johnson CN]]
[[Category: Shaw, B R]]
[[Category: Shaw BR]]
[[Category: Spring, A M]]
[[Category: Spring AM]]
[[Category: Dna-rna complex]]
[[Category: Nucleic acid heteroduplex]]
[[Category: Rnase h1 activity]]

Latest revision as of 09:54, 1 May 2024

DNA / RNA Hybrid containing a central stereo specific Sp borano phosphate linkageDNA / RNA Hybrid containing a central stereo specific Sp borano phosphate linkage

Structural highlights

2lb4 is a 2 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT
Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2lb4&oldid=4136286"