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| | <StructureSection load='1wsf' size='340' side='right'caption='[[1wsf]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='1wsf' size='340' side='right'caption='[[1wsf]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1wsf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WSF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WSF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1wsf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WSF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WSF FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wse|1wse]], [[1wsg|1wsg]], [[1wsh|1wsh]], [[1wsi|1wsi]], [[1wsj|1wsj]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [https://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=1wsf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wsf OCA], [https://pdbe.org/1wsf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wsf RCSB], [https://www.ebi.ac.uk/pdbsum/1wsf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wsf 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=1wsf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wsf OCA], [https://pdbe.org/1wsf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wsf RCSB], [https://www.ebi.ac.uk/pdbsum/1wsf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wsf ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/RNH_ECOLI RNH_ECOLI]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. RNase H participates in DNA replication; it helps to specify the origin of genomic replication by suppressing initiation at origins other than the oriC locus; along with the 5'-3' exonuclease of pol1, it removes RNA primers from the Okazaki fragments of lagging strand synthesis; and it defines the origin of replication for ColE1-type plasmids by specific cleavage of an RNA preprimer.[HAMAP-Rule:MF_00042]
| + | [https://www.uniprot.org/uniprot/RNH_ECOLI RNH_ECOLI] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. RNase H participates in DNA replication; it helps to specify the origin of genomic replication by suppressing initiation at origins other than the oriC locus; along with the 5'-3' exonuclease of pol1, it removes RNA primers from the Okazaki fragments of lagging strand synthesis; and it defines the origin of replication for ColE1-type plasmids by specific cleavage of an RNA preprimer.[HAMAP-Rule:MF_00042] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ribonuclease H]]
| + | [[Category: Kanaya S]] |
| - | [[Category: Kanaya, S]] | + | [[Category: Matsumura H]] |
| - | [[Category: Matsumura, H]] | + | [[Category: Takano K]] |
| - | [[Category: Takano, K]] | + | [[Category: Tsunaka Y]] |
| - | [[Category: Tsunaka, Y]] | + | [[Category: Yamagata Y]] |
| - | [[Category: Yamagata, Y]] | + | |
| - | [[Category: Active-site mutant]]
| + | |
| - | [[Category: Co-crystal structure with mn2+]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Metal fluctuation model]]
| + | |
| - | [[Category: Rnase h]]
| + | |
| Structural highlights
Function
RNH_ECOLI Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. RNase H participates in DNA replication; it helps to specify the origin of genomic replication by suppressing initiation at origins other than the oriC locus; along with the 5'-3' exonuclease of pol1, it removes RNA primers from the Okazaki fragments of lagging strand synthesis; and it defines the origin of replication for ColE1-type plasmids by specific cleavage of an RNA preprimer.[HAMAP-Rule:MF_00042]
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
Escherichia coli RNase HI has two Mn(2+)-binding sites. Site 1 is formed by Asp10, Glu48, and Asp70, and site 2 is formed by Asp10 and Asp134. Site 1 and site 2 have been proposed to be an activation site and an attenuation site, respectively. However, Glu48 and Asp134 are dispensable for Mn(2+)-dependent activity. In order to identify the Mn(2+)-binding sites of the mutant proteins at Glu48 and/or Asp134, the crystal structures of the mutant proteins E48A-RNase HI*, D134A-RNase HI*, and E48A/D134N-RNase HI* in complex with Mn(2+) were determined. In E48A-RNase HI*, Glu48 and Lys87 are replaced by Ala. In D134A-RNase HI*, Asp134 and Lys87 are replaced by Ala. In E48A/D134N-RNase HI*, Glu48 and Lys87 are replaced by Ala and Asp134 is replaced by Asn. All crystals had two or four protein molecules per asymmetric unit and at least two of which had detectable manganese ions. These structures indicated that only one manganese ion binds to the various positions around the center of the active-site pocket. These positions are different from one another, but none of them is similar to site 1. The temperature factors of these manganese ions were considerably larger than those of the surrounding residues. These results suggest that the first manganese ion required for activation of the wild-type protein fluctuates among various positions around the center of the active-site pockets. We propose that this fluctuation is responsible for efficient hydrolysis of the substrates by the protein (metal fluctuation model). The binding position of the first manganese ion is probably forced to shift to site 1 or site 2 upon binding of the second manganese ion.
Identification of single Mn(2+) binding sites required for activation of the mutant proteins of E.coli RNase HI at Glu48 and/or Asp134 by X-ray crystallography.,Tsunaka Y, Takano K, Matsumura H, Yamagata Y, Kanaya S J Mol Biol. 2005 Feb 4;345(5):1171-83. Epub 2004 Dec 16. PMID:15644213[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Tsunaka Y, Takano K, Matsumura H, Yamagata Y, Kanaya S. Identification of single Mn(2+) binding sites required for activation of the mutant proteins of E.coli RNase HI at Glu48 and/or Asp134 by X-ray crystallography. J Mol Biol. 2005 Feb 4;345(5):1171-83. Epub 2004 Dec 16. PMID:15644213 doi:http://dx.doi.org/10.1016/j.jmb.2004.11.007
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