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| | <StructureSection load='7vse' size='340' side='right'caption='[[7vse]], [[Resolution|resolution]] 2.08Å' scene=''> | | <StructureSection load='7vse' size='340' side='right'caption='[[7vse]], [[Resolution|resolution]] 2.08Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[7vse]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VSE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VSE FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7vse]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VSE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VSE FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.08Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7vsa|7vsa]], [[7vsb|7vsb]], [[7vsc|7vsc]], [[7vsd|7vsd]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7vse FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vse OCA], [https://pdbe.org/7vse PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vse RCSB], [https://www.ebi.ac.uk/pdbsum/7vse PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vse 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=7vse FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vse OCA], [https://pdbe.org/7vse PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vse RCSB], [https://www.ebi.ac.uk/pdbsum/7vse PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vse 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] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 7vse" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 7vse" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Escherichia coli K-12]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ribonuclease H]]
| + | [[Category: Liao Z]] |
| - | [[Category: Liao, Z]] | + | [[Category: Oyama T]] |
| - | [[Category: Oyama, T]] | + | |
| - | [[Category: Endonuclease]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Metalloenzyme]]
| + | |
| 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]
Publication Abstract from PubMed
The ribonuclease (RNase) H family of enzymes catalyze the specific cleavage of RNA strands of RNA/DNA hybrid duplexes and play an important role in DNA replication and repair. Since the first report of the crystal structure of RNase HI, its catalytic mechanisms, which require metal ions, have been discussed based on numerous structural and functional analyses, including X-ray crystallography. In contrast, the function of the conserved histidine residue (His124 in Escherichia coli) in the flexible loop around the active site remains poorly understood, although an important role was suggested by NMR analyses. Here, novel high-resolution X-ray crystal structures of E. coli RNase HI are described, with a particular focus on the interactions of divalent cations with His124 oriented towards the active site. The enzyme-Mg(2+) complex contains two metal ions in the active site, one of which has previously been observed. The second ion lies alongside the first and binds to His124 in an octahedral coordination scheme. In the enzyme-Zn(2+) complex a single metal ion was found to bind to the active site, showing a tetrahedral coordination geometry with the surrounding atoms, including His124. These results provide structural evidence that His124 plays a crucial role in the catalytic activity of RNase HI by interacting weakly and transiently with metal ions in the catalytic center.
Pivotal role of a conserved histidine in Escherichia coli ribonuclease HI as proposed by X-ray crystallography.,Liao Z, Oyama T, Kitagawa Y, Katayanagi K, Morikawa K, Oda M Acta Crystallogr D Struct Biol. 2022 Mar 1;78(Pt 3):390-398. doi:, 10.1107/S2059798322000870. Epub 2022 Feb 23. PMID:35234152[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Liao Z, Oyama T, Kitagawa Y, Katayanagi K, Morikawa K, Oda M. Pivotal role of a conserved histidine in Escherichia coli ribonuclease HI as proposed by X-ray crystallography. Acta Crystallogr D Struct Biol. 2022 Mar 1;78(Pt 3):390-398. doi:, 10.1107/S2059798322000870. Epub 2022 Feb 23. PMID:35234152 doi:http://dx.doi.org/10.1107/S2059798322000870
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