5swm: Difference between revisions

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<StructureSection load='5swm' size='340' side='right'caption='[[5swm]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
<StructureSection load='5swm' size='340' side='right'caption='[[5swm]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5swm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_alcalophilus_subsp._halodurans"_boyer_et_al._1973 "bacillus alcalophilus subsp. halodurans" boyer et al. 1973]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SWM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SWM FirstGlance]. <br>
<table><tr><td colspan='2'>[[5swm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans Alkalihalobacillus halodurans] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SWM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SWM FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AF2:2-DEOXY-2-FLUOROADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>AF2</scene>, <scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=CFZ:2-DEOXY-2-FLUOROCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>CFZ</scene>, <scene name='pdbligand=GF2:2-DEOXY-2-FLUOROGUANOSINE+5-(DIHYDROGEN+PHOSPHATE)'>GF2</scene>, <scene name='pdbligand=UFT:2-DEOXY-2-FLUOROURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UFT</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AF2:2-DEOXY-2-FLUOROADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>AF2</scene>, <scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=CFZ:2-DEOXY-2-FLUOROCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>CFZ</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GF2:2-DEOXY-2-FLUOROGUANOSINE+5-(DIHYDROGEN+PHOSPHATE)'>GF2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=UFT:2-DEOXY-2-FLUOROURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UFT</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rnhA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86665 "Bacillus alcalophilus subsp. halodurans" Boyer et al. 1973])</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=5swm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5swm OCA], [https://pdbe.org/5swm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5swm RCSB], [https://www.ebi.ac.uk/pdbsum/5swm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5swm ProSAT]</span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5swm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5swm OCA], [http://pdbe.org/5swm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5swm RCSB], [http://www.ebi.ac.uk/pdbsum/5swm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5swm ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/RNH1_BACHD RNH1_BACHD]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.  
[https://www.uniprot.org/uniprot/RNH1_HALH5 RNH1_HALH5] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.<ref>PMID:15989951</ref>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus alcalophilus subsp. halodurans boyer et al. 1973]]
[[Category: Alkalihalobacillus halodurans]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Ribonuclease H]]
[[Category: Synthetic construct]]
[[Category: Egli, M]]
[[Category: Egli M]]
[[Category: Pallan, P S]]
[[Category: Pallan PS]]
[[Category: Hydrolase-rna-dna complex]]
[[Category: Rna/dna hybrid]]
[[Category: Rnase h]]

Latest revision as of 15:49, 4 October 2023

BACILLUS HALODURANS RNASE H MUTANT D132N IN COMPLEX WITH 12-MER FRNA/DNA HYBRIDBACILLUS HALODURANS RNASE H MUTANT D132N IN COMPLEX WITH 12-MER FRNA/DNA HYBRID

Structural highlights

5swm is a 4 chain structure with sequence from Alkalihalobacillus halodurans and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.5Å
Ligands:, , , , , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RNH1_HALH5 Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.[1]

Publication Abstract from PubMed

RNase H1 cleaves the RNA strand of RNA:DNA hybrids. Replacement of RNA 2'-hydroxyls by fluorine (FRNA) is commonly used to stabilize aptamers and siRNAs. However, FRNA:DNA hybrids fail to elicit RNase H activity. The underlying reasons are unclear, as 2'-OH groups are not directly involved in cleavage. We determined the crystal structure of Bacillus halodurans RNase H bound to a FRNA:DNA hybrid. The structure points to dynamic (slippage of the FRNA:DNA hybrid relative to the enzyme), geometric (different curvatures of FRNA:DNA and RNA:DNA hybrids), and electronic reasons (Mg2+ absent from the active site of the FRNA:DNA complex) for the loss of RNaseH activity.

Limits of RNA 2'-OH Mimicry by Fluorine: Crystal Structure of Bacillus halodurans RNase H Bound to a 2'-FRNA:DNA Hybrid.,Pallan PS, Prakash TP, de Leon AR, Egli M Biochemistry. 2016 Sep 14. PMID:27611889[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Nowotny M, Gaidamakov SA, Crouch RJ, Yang W. Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis. Cell. 2005 Jul 1;121(7):1005-16. PMID:15989951 doi:http://dx.doi.org/10.1016/j.cell.2005.04.024
  2. ↑ Pallan PS, Prakash TP, de Leon AR, Egli M. Limits of RNA 2'-OH Mimicry by Fluorine: Crystal Structure of Bacillus halodurans RNase H Bound to a 2'-FRNA:DNA Hybrid. Biochemistry. 2016 Sep 14. PMID:27611889 doi:http://dx.doi.org/10.1021/acs.biochem.6b00849

5swm, resolution 1.50Å

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