7vsb: Difference between revisions
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==E. coli Ribonuclease HI in complex with one Zn2+ (His124 N-delta binding)== | ==E. coli Ribonuclease HI in complex with one Zn2+ (His124 N-delta binding)== | ||
<StructureSection load='7vsb' size='340' side='right'caption='[[7vsb]]' scene=''> | <StructureSection load='7vsb' size='340' side='right'caption='[[7vsb]], [[Resolution|resolution]] 1.84Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VSB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VSB FirstGlance]. <br> | <table><tr><td colspan='2'>[[7vsb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VSB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VSB FirstGlance]. <br> | ||
</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=7vsb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vsb OCA], [https://pdbe.org/7vsb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vsb RCSB], [https://www.ebi.ac.uk/pdbsum/7vsb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vsb ProSAT]</span></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=7vsb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vsb OCA], [https://pdbe.org/7vsb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vsb RCSB], [https://www.ebi.ac.uk/pdbsum/7vsb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vsb ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== 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] | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:35234152</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7vsb" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Liao Z]] | [[Category: Ribonuclease H]] | ||
[[Category: Oyama T]] | [[Category: Liao, Z]] | ||
[[Category: Oyama, T]] | |||
[[Category: Endonuclease]] | |||
[[Category: Hydrolase]] | |||
[[Category: Metalloenzyme]] | |||
Revision as of 10:26, 16 March 2022
E. coli Ribonuclease HI in complex with one Zn2+ (His124 N-delta binding)E. coli Ribonuclease HI in complex with one Zn2+ (His124 N-delta binding)
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 PubMedThe 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. References
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