7vsd - Revision history

OCA at 17:31, 29 November 2023

2023-11-29T17:31:43Z

← Older revision		Revision as of 17:31, 29 November 2023
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	<StructureSection load='7vsd' size='340' side='right'caption='[[7vsd]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='7vsd' size='340' side='right'caption='[[7vsd]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7vsd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VSD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VSD FirstGlance]. <br>		<table><tr><td colspan='2'>[[7vsd]] 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=7VSD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VSD FirstGlance]. <br>
	</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>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.7Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=7vsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vsd OCA], [https://pdbe.org/7vsd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vsd RCSB], [https://www.ebi.ac.uk/pdbsum/7vsd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vsd 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=7vsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vsd OCA], [https://pdbe.org/7vsd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vsd RCSB], [https://www.ebi.ac.uk/pdbsum/7vsd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vsd 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 7vsd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7vsd" 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~~]]

OCA at 07:26, 16 March 2022

2022-03-16T07:26:31Z

← Older revision		Revision as of 07:26, 16 March 2022
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	==E. coli Ribonuclease HI in complex with one Mg2+ (2)==		==E. coli Ribonuclease HI in complex with one Mg2+ (2)==
	<StructureSection load='7vsd' size='340' side='right'caption='[[7vsd]]' scene=''>		<StructureSection load='7vsd' size='340' side='right'caption='[[7vsd]], [[Resolution\|resolution]] 1.70Å' 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=7VSD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VSD FirstGlance]. <br>		<table><tr><td colspan='2'>[[7vsd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VSD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VSD 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=7vsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vsd OCA], [https://pdbe.org/7vsd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vsd RCSB], [https://www.ebi.ac.uk/pdbsum/7vsd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vsd 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7vsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vsd OCA], [https://pdbe.org/7vsd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vsd RCSB], [https://www.ebi.ac.uk/pdbsum/7vsd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vsd 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 7vsd" 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]]

OCA at 06:23, 2 March 2022

2022-03-02T06:23:38Z

← Older revision		Revision as of 06:23, 2 March 2022
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	~~'''Unreleased structure'''~~

	~~The entry 7vsd is ON HOLD until Paper Publication~~		==E. coli Ribonuclease HI in complex with one Mg2+ (2)==
			<StructureSection load='7vsd' size='340' side='right'caption='[[7vsd]]' scene=''>
	~~Authors: Liao, Z., Oyama, T.~~		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VSD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VSD FirstGlance]. <br>
	~~Description:~~ E. coli Ribonuclease HI in complex with one Mg2+ (2)		</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=7vsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vsd OCA], [https://pdbe.org/7vsd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vsd RCSB], [https://www.ebi.ac.uk/pdbsum/7vsd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vsd ProSAT]</span></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		</table>
	[[Category: Liao, Z]]		__TOC__
	[[Category: Oyama, T]]		</StructureSection>
			[[Category: Large Structures]]
			[[Category: Liao Z]]
			[[Category: Oyama T]]

OCA at 12:28, 29 December 2021

2021-12-29T12:28:38Z

← Older revision		Revision as of 12:28, 29 December 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7vsd is ON HOLD		The entry 7vsd is ON HOLD until Paper Publication

	Authors: Liao, Z., Oyama, T.		Authors: Liao, Z., Oyama, T.

OCA: Protected "7vsd" [edit=sysop:move=sysop]

2021-11-03T13:02:30Z

Protected "7vsd" [edit=sysop:move=sysop]

← Older revision	Revision as of 13:02, 3 November 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7vsd is ON HOLD Authors: Liao, Z., Oyama, T. Description: E. coli Ribonuclease HI in complex with one Mg2+ (2) Category: Unreleased Structures ...

2021-11-03T13:02:28Z

New page: '''Unreleased structure''' The entry 7vsd is ON HOLD Authors: Liao, Z., Oyama, T. Description: E. coli Ribonuclease HI in complex with one Mg2+ (2) Category: Unreleased Structures ...

New page

'''Unreleased structure'''

The entry 7vsd is ON HOLD

Authors: Liao, Z., Oyama, T.

Description: E. coli Ribonuclease HI in complex with one Mg2+ (2)
[[Category: Unreleased Structures]]
[[Category: Liao, Z]]
[[Category: Oyama, T]]