6dp2 - Revision history

OCA at 06:11, 11 October 2023

OCA — Wed, 11 Oct 2023 06:11:41 GMT

←Older revision		Revision as of 06:11, 11 October 2023
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	==Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 7.5 mM Mg2+ and 75 mM K+ for 40 s at 21 C==		==Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 7.5 mM Mg2+ and 75 mM K+ for 40 s at 21 C==
-	<StructureSection load='6dp2' size='340' side='right' caption='[[6dp2]], [[Resolution\|resolution]] 1.66Å' scene=''>	+	<StructureSection load='6dp2' size='340' side='right'caption='[[6dp2]], [[Resolution\|resolution]] 1.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dp2]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bachd Bachd~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DP2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DP2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dp2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans_C-125 Alkalihalobacillus halodurans C-125] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DP2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DP2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.662Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnhA, BH0863 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272558 BACHD])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6dp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dp2 OCA], [https://pdbe.org/6dp2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dp2 RCSB], [https://www.ebi.ac.uk/pdbsum/6dp2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dp2 ProSAT]</span></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=6dp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dp2 OCA], [~~http~~://pdbe.org/6dp2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dp2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dp2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dp2 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~RNH1_BACHD RNH1_BACHD]~~] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.	+	[https://www.uniprot.org/uniprot/RNH1_HALH5 RNH1_HALH5] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.<ref>PMID:15989951</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6dp2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6dp2" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bachd]]~~	+	[[Category: Alkalihalobacillus halodurans C-125]]
-	~~[[Category: Ribonuclease H]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Samara, N L]]~~	+	[[Category: Synthetic construct]]
-	~~[[Category: Yang, W]]~~	+	[[Category: Samara NL]]
-	~~[[Category: Hydrolase-dna~~-~~rna complex~~]]	+	[[Category: Yang W]]
-	[[Category: ~~In crystallo catalysis~~]]	+
-	[[Category: ~~Metal dependent catalysis~~]]	+
-	[[Category: ~~Protein-rna-dna complex~~]]	+
-	[[Category: ~~Rna hydrolysis~~]]	+

OCA at 06:36, 22 August 2018

OCA — Wed, 22 Aug 2018 06:36:16 GMT

←Older revision		Revision as of 06:36, 22 August 2018
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	<StructureSection load='6dp2' size='340' side='right' caption='[[6dp2]], [[Resolution\|resolution]] 1.66Å' scene=''>		<StructureSection load='6dp2' size='340' side='right' caption='[[6dp2]], [[Resolution\|resolution]] 1.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dp2]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DP2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DP2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dp2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bachd Bachd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DP2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DP2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnhA, BH0863 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272558 BACHD])</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>		<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>
	<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=6dp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dp2 OCA], [http://pdbe.org/6dp2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dp2 RCSB], [http://www.ebi.ac.uk/pdbsum/6dp2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dp2 ProSAT]</span></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=6dp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dp2 OCA], [http://pdbe.org/6dp2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dp2 RCSB], [http://www.ebi.ac.uk/pdbsum/6dp2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dp2 ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RNH1_BACHD RNH1_BACHD]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.		[[http://www.uniprot.org/uniprot/RNH1_BACHD RNH1_BACHD]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Catalysis by members of the RNase H superfamily of enzymes is generally believed to require only two Mg(2+) ions that are coordinated by active-site carboxylates. By examining the catalytic process of Bacillus halodurans RNase H1 in crystallo, however, we found that the two canonical Mg(2+) ions and an additional K(+) failed to align the nucleophilic water for RNA cleavage. Substrate alignment and product formation required a second K(+) and a third Mg(2+), which replaced the first K(+) and departed immediately after cleavage. A third transient Mg(2+) has also been observed for DNA synthesis, but in that case it coordinates the leaving group instead of the nucleophile as in the case of the RNase H1 hydrolysis reaction. These transient cations have no contact with the enzymes. Other DNA and RNA enzymes that catalyze consecutive cleavage and strand-transfer reactions in a single active site may similarly require cation trafficking coordinated by the substrate.
		+
		+	Cation trafficking propels RNA hydrolysis.,Samara NL, Yang W Nat Struct Mol Biol. 2018 Aug;25(8):715-721. doi: 10.1038/s41594-018-0099-4. Epub, 2018 Aug 3. PMID:30076410<ref>PMID:30076410</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6dp2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bachd]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
	[[Category: Samara, N L]]		[[Category: Samara, N L]]

OCA at 16:18, 15 August 2018

OCA — Wed, 15 Aug 2018 16:18:23 GMT

←Older revision		Revision as of 16:18, 15 August 2018
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-	'''Unreleased structure'''

-	~~The entry 6dp2 is ON HOLD until Paper Publication~~	+	==Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 7.5 mM Mg2+ and 75 mM K+ for 40 s at 21 C==
-		+	<StructureSection load='6dp2' size='340' side='right' caption='[[6dp2]], [[Resolution\|resolution]] 1.66Å' scene=''>
-	~~Authors: Samara, N.L., Yang, W.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6dp2]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DP2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DP2 FirstGlance]. <br>
-	~~Description:~~ Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 7.5 mM Mg2+ and 75 mM K+ for 40 s at 21 C	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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>
-	[[Category: Samara, N.L]]	+	<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=6dp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dp2 OCA], [http://pdbe.org/6dp2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dp2 RCSB], [http://www.ebi.ac.uk/pdbsum/6dp2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dp2 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RNH1_BACHD RNH1_BACHD]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ribonuclease H]]
		+	[[Category: Samara, N L]]
	[[Category: Yang, W]]		[[Category: Yang, W]]
		+	[[Category: Hydrolase-dna-rna complex]]
		+	[[Category: In crystallo catalysis]]
		+	[[Category: Metal dependent catalysis]]
		+	[[Category: Protein-rna-dna complex]]
		+	[[Category: Rna hydrolysis]]

OCA at 19:46, 9 August 2018

OCA — Thu, 09 Aug 2018 19:46:19 GMT

←Older revision		Revision as of 19:46, 9 August 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6dp2 is ON HOLD	+	The entry 6dp2 is ON HOLD until Paper Publication

	Authors: Samara, N.L., Yang, W.		Authors: Samara, N.L., Yang, W.

OCA: Protected "6dp2" [edit=sysop:move=sysop]

OCA — Wed, 20 Jun 2018 04:04:29 GMT

Protected "6dp2" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:04, 20 June 2018

OCA: New page: '''Unreleased structure''' The entry 6dp2 is ON HOLD Authors: Samara, N.L., Yang, W. Description: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hy...

OCA — Wed, 20 Jun 2018 04:04:27 GMT

New page: '''Unreleased structure''' The entry 6dp2 is ON HOLD Authors: Samara, N.L., Yang, W. Description: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hy...

New page

'''Unreleased structure'''

The entry 6dp2 is ON HOLD

Authors: Samara, N.L., Yang, W.

Description: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 7.5 mM Mg2+ and 75 mM K+ for 40 s at 21 C
[[Category: Unreleased Structures]]
[[Category: Samara, N.L]]
[[Category: Yang, W]]