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| | <StructureSection load='1zbi' size='340' side='right'caption='[[1zbi]], [[Resolution|resolution]] 1.85Å' scene=''> | | <StructureSection load='1zbi' size='340' side='right'caption='[[1zbi]], [[Resolution|resolution]] 1.85Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1zbi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bachd Bachd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZBI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZBI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1zbi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans_C-125 Alkalihalobacillus halodurans C-125]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZBI FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.85Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1zbf|1zbf]], [[1zbl|1zbl]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=1zbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zbi OCA], [https://pdbe.org/1zbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zbi RCSB], [https://www.ebi.ac.uk/pdbsum/1zbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zbi ProSAT]</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=1zbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zbi OCA], [http://pdbe.org/1zbi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zbi RCSB], [http://www.ebi.ac.uk/pdbsum/1zbi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1zbi 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> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] | | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] |
| - | *[[Temp|Temp]] | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bachd]] | + | [[Category: Alkalihalobacillus halodurans C-125]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ribonuclease H]]
| + | [[Category: Crouch RJ]] |
| - | [[Category: Crouch, R J]] | + | [[Category: Gaidamakov SA]] |
| - | [[Category: Gaidamakov, S A]] | + | [[Category: Nowotny M]] |
| - | [[Category: Nowotny, M]] | + | [[Category: Yang W]] |
| - | [[Category: Yang, W]] | + | |
| - | [[Category: Dde motif]]
| + | |
| - | [[Category: Hydrolase-rna-dna complex]]
| + | |
| - | [[Category: Rna/dna hybrid]]
| + | |
| - | [[Category: Rnase h]]
| + | |
| Structural highlights
Function
RNH1_HALH5 Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
RNase H belongs to a nucleotidyl-transferase superfamily, which includes transposase, retroviral integrase, Holliday junction resolvase, and RISC nuclease Argonaute. We report the crystal structures of RNase H complexed with an RNA/DNA hybrid and a mechanism for substrate recognition and two-metal-ion-dependent catalysis. RNase H specifically recognizes the A form RNA strand and the B form DNA strand. Structure comparisons lead us to predict the catalytic residues of Argonaute and conclude that two-metal-ion catalysis is a general feature of the superfamily. In nucleases, the two metal ions are asymmetrically coordinated and have distinct roles in activating the nucleophile and stabilizing the transition state. In transposases, they are symmetrically coordinated and exchange roles to alternately activate a water and a 3'-OH for successive strand cleavage and transfer by a ping-pong mechanism.
Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis.,Nowotny M, Gaidamakov SA, Crouch RJ, Yang W Cell. 2005 Jul 1;121(7):1005-16. PMID:15989951[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ 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
- ↑ 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
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