6dor - Revision history

OCA at 06:11, 11 October 2023

2023-10-11T06:11:17Z

←Older revision		Revision as of 06:11, 11 October 2023
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	<StructureSection load='6dor' size='340' side='right'caption='[[6dor]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='6dor' size='340' side='right'caption='[[6dor]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dor]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DOR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6DOR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dor]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans Alkalihalobacillus halodurans] 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=6DOR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DOR FirstGlance]. <br>
-	</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>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 1.5Å</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='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>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6dor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dor OCA], [~~http~~://pdbe.org/6dor PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dor RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dor PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dor 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=6dor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dor OCA], [https://pdbe.org/6dor PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dor RCSB], [https://www.ebi.ac.uk/pdbsum/6dor PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dor 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 ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Alkalihalobacillus halodurans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ribonuclease H~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Samara~~, N L~~]]	+	[[Category: Samara NL]]
-	[[Category: Yang, W]]	+	[[Category: Yang W]]
-	~~[[Category: Divalent cation]]~~	+
-	~~[[Category: Double helix]]~~	+
-	~~[[Category: Hydrolase-dna-rna complex]]~~	+
-	~~[[Category: In crystallo catalysis]]~~	+
-	~~[[Category: Metal dependent catalysis]]~~	+
-	~~[[Category: Monovalent cation]]~~	+
-	~~[[Category: Protein-rna-dna complex]]~~	+
-	~~[[Category: Rna hydrolysis~~]]	+

OCA at 09:06, 11 November 2020

2020-11-11T09:06:40Z

←Older revision		Revision as of 09:06, 11 November 2020
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	==Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 300 mM K+ for 120 s at 21 C (dataset 1)==		==Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 300 mM K+ for 120 s at 21 C (dataset 1)==
-	<StructureSection load='6dor' size='340' side='right' caption='[[6dor]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='6dor' size='340' side='right'caption='[[6dor]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dor]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DOR OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DOR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dor]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DOR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6DOR 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>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>	+	</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>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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='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=6dor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dor OCA], [http://pdbe.org/6dor PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dor RCSB], [http://www.ebi.ac.uk/pdbsum/6dor PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dor ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6dor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dor OCA], [http://pdbe.org/6dor PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dor RCSB], [http://www.ebi.ac.uk/pdbsum/6dor PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dor ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 6dor" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6dor" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
	[[Category: Samara, N L]]		[[Category: Samara, N L]]

OCA at 16:17, 15 August 2018

2018-08-15T16:17:43Z

←Older revision		Revision as of 16:17, 15 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6dor is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 300 mM K+ for 120 s at 21 C (dataset 1)==
		+	<StructureSection load='6dor' size='340' side='right' caption='[[6dor]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6dor]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DOR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DOR 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>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6dor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dor OCA], [http://pdbe.org/6dor PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dor RCSB], [http://www.ebi.ac.uk/pdbsum/6dor PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dor 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.
		+	<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.

-	~~Authors:~~ Samara, N.L., ~~Yang, W~~.	+	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>

-	~~Description: Crystal Structure~~ of ~~Bacillus Halodurans Ribonuclease H1 in Complex with an RNA~~/~~DNA Hybrid~~: ~~Reaction in 2 mM Mg2+ and 300 mM K+ for 120 s at 21 C (dataset 1)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Samara, N.L]]	+	<div class="pdbe-citations 6dor" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ribonuclease H]]
		+	[[Category: Samara, N L]]
	[[Category: Yang, W]]		[[Category: Yang, W]]
		+	[[Category: Divalent cation]]
		+	[[Category: Double helix]]
		+	[[Category: Hydrolase-dna-rna complex]]
		+	[[Category: In crystallo catalysis]]
		+	[[Category: Metal dependent catalysis]]
		+	[[Category: Monovalent cation]]
		+	[[Category: Protein-rna-dna complex]]
		+	[[Category: Rna hydrolysis]]

OCA at 05:48, 25 July 2018

2018-07-25T05:48:13Z

←Older revision		Revision as of 05:48, 25 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

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

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

2018-06-20T04:03:55Z

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

←Older revision

Revision as of 04:03, 20 June 2018

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

2018-06-20T04:03:53Z

New page: '''Unreleased structure''' The entry 6dor 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 6dor 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 2 mM Mg2+ and 300 mM K+ for 120 s at 21 C (dataset 1)
[[Category: Unreleased Structures]]
[[Category: Samara, N.L]]
[[Category: Yang, W]]