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| | <StructureSection load='1kva' size='340' side='right'caption='[[1kva]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='1kva' size='340' side='right'caption='[[1kva]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1kva]] is a 1 chain structure with sequence from [http://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=1KVA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KVA FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1kva]] is a 1 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=1KVA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KVA FirstGlance]. <br> |
| - | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</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=1kva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kva OCA], [http://pdbe.org/1kva PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kva RCSB], [http://www.ebi.ac.uk/pdbsum/1kva PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kva 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=1kva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kva OCA], [https://pdbe.org/1kva PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kva RCSB], [https://www.ebi.ac.uk/pdbsum/1kva PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kva ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kv/1kva_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kv/1kva_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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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: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ribonuclease H]]
| + | [[Category: Haruki M]] |
| - | [[Category: Haruki, M]] | + | [[Category: Jeanteur D]] |
| - | [[Category: Jeanteur, D]] | + | [[Category: Kanaya S]] |
| - | [[Category: Kanaya, S]] | + | [[Category: Kashiwagi T]] |
| - | [[Category: Kashiwagi, T]] | + | [[Category: Katayanagi K]] |
| - | [[Category: Katayanagi, K]] | + | [[Category: Morikawa K]] |
| - | [[Category: Morikawa, K]] | + | |
| - | [[Category: Endoribonuclease]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Mutant]]
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| 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
Three mutants of Escherichia coli ribonuclease HI, in which an invariant acidic residue Asp134 was replaced, were crystallized, and their three-dimensional structures were determined by X-ray crystallography. The D134A mutant is completely inactive, whereas the other two mutants, D134H and D134N, retain 59 and 90% activities relative to the wild-type, respectively. The overall structures of these three mutant proteins are identical with that of the wild-type enzyme, except for local conformational changes of the flexible loops. The ribonuclease H family has a common active site, which is composed of four invariant acidic residues (Asp10, Glu48, Asp70 and Asp134 in E.coli ribonuclease HI), and their relative positions in the mutants, even including the side-chain atoms, are almost the same as those in the wild-type. The positions of the delta-polar atoms at residue 134 in the wild-type, as well as D134H and D134N, coincide well with each other. They are located near the imidazole side chain of His124, which is assumed to participate in the catalytic reaction, in addition to the four invariant acidic residues. Combined with the pH profiles of the enzymatic activities of the two other mutants, H124A and H124A/D134N, the crystallographic results allow us to propose a new catalytic mechanism of ribonuclease H, which includes the roles for Asp134 and His124.
Proposal for new catalytic roles for two invariant residues in Escherichia coli ribonuclease HI.,Kashiwagi T, Jeanteur D, Haruki M, Katayanagi K, Kanaya S, Morikawa K Protein Eng. 1996 Oct;9(10):857-67. PMID:8931125[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kashiwagi T, Jeanteur D, Haruki M, Katayanagi K, Kanaya S, Morikawa K. Proposal for new catalytic roles for two invariant residues in Escherichia coli ribonuclease HI. Protein Eng. 1996 Oct;9(10):857-67. PMID:8931125
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