6hz8 - Revision history

OCA at 01:35, 11 April 2020

OCA — Sat, 11 Apr 2020 01:35:51 GMT

←Older revision		Revision as of 01:35, 11 April 2020
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	<SX load='6hz8' size='340' side='right' viewer='molstar' caption='[[6hz8]], [[Resolution\|resolution]] 4.30Å' scene=''>		<SX load='6hz8' size='340' side='right' viewer='molstar' caption='[[6hz8]], [[Resolution\|resolution]] 4.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6hz8]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6HZ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6hz8]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6HZ8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</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" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</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">mcrB, rglB, b4346, JW5871 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), mcrC, b4345, JW5789 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mcrB, rglB, b4346, JW5871 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), mcrC, b4345, JW5789 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6hz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hz8 OCA], [http://pdbe.org/6hz8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hz8 RCSB], [http://www.ebi.ac.uk/pdbsum/6hz8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hz8 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=6hz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hz8 OCA], [http://pdbe.org/6hz8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hz8 RCSB], [http://www.ebi.ac.uk/pdbsum/6hz8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hz8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 21:58, 6 March 2020

OCA — Fri, 06 Mar 2020 21:58:26 GMT

←Older revision		Revision as of 21:58, 6 March 2020
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	==Structure of McrBC without DNA binding domains (Class 4)==		==Structure of McrBC without DNA binding domains (Class 4)==
-	<~~StructureSection~~ load='6hz8' size='340' side='right'caption='[[6hz8]], [[Resolution\|resolution]] 4.30Å' scene=''>	+	<SX load='6hz8' size='340' side='right' viewer='molstar' caption='[[6hz8]], [[Resolution\|resolution]] 4.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6hz8]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HZ8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6hz8]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HZ8 FirstGlance]. <br>
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	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Ecoli]]		[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 07:55, 6 November 2019

OCA — Wed, 06 Nov 2019 07:55:11 GMT

←Older revision		Revision as of 07:55, 6 November 2019
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	<StructureSection load='6hz8' size='340' side='right'caption='[[6hz8]], [[Resolution\|resolution]] 4.30Å' scene=''>		<StructureSection load='6hz8' size='340' side='right'caption='[[6hz8]], [[Resolution\|resolution]] 4.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6hz8]] is a 14 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HZ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6hz8]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HZ8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</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=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</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">mcrB, rglB, b4346, JW5871 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), mcrC, b4345, JW5789 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6hz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hz8 OCA], [http://pdbe.org/6hz8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hz8 RCSB], [http://www.ebi.ac.uk/pdbsum/6hz8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hz8 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=6hz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hz8 OCA], [http://pdbe.org/6hz8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hz8 RCSB], [http://www.ebi.ac.uk/pdbsum/6hz8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hz8 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Amunts, A]]		[[Category: Amunts, A]]

OCA at 06:09, 24 July 2019

OCA — Wed, 24 Jul 2019 06:09:49 GMT

←Older revision		Revision as of 06:09, 24 July 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6hz8 is ~~ON HOLD~~	+	==Structure of McrBC without DNA binding domains (Class 4)==
		+	<StructureSection load='6hz8' size='340' side='right'caption='[[6hz8]], [[Resolution\|resolution]] 4.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6hz8]] is a 14 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HZ8 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=6hz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hz8 OCA], [http://pdbe.org/6hz8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hz8 RCSB], [http://www.ebi.ac.uk/pdbsum/6hz8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hz8 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MCRB_ECOLI MCRB_ECOLI]] Recognizes N4- and C5-methylcytosine (and 5-hydroxy-methylcytosines) produced by a broad range of DNA methylases and appears to act against 5-methylcytosine preceded by a purine residue. Binds to DNA containing methylated cytosines; also binds to GTP. Isoform 33 kDa is less active than isoform 51 kDa and may play a role in regulating the activity of isoform 51 kDa by competing with it in DNA and protein binding abilities. [[http://www.uniprot.org/uniprot/MCRC_ECOLI MCRC_ECOLI]] Modifies the specificity of McrB restriction by expanding the range of modified sequences restricted. Does not bind to DNA.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The AAA+ GTPase McrB powers DNA cleavage by the endonuclease McrC. The GTPase itself is activated by McrC. The architecture of the GTPase and nuclease complex, and the mechanism of their activation remained unknown. Here, we report a 3.6 A structure of a GTPase-active and DNA-binding deficient construct of McrBC. Two hexameric rings of McrB are bridged by McrC dimer. McrC interacts asymmetrically with McrB protomers and inserts a stalk into the pore of the ring, reminiscent of the gamma subunit complexed to alpha3beta3 of F1-ATPase. Activation of the GTPase involves conformational changes of residues essential for hydrolysis. Three consecutive nucleotide-binding pockets are occupied by the GTP analogue 5'-guanylyl imidodiphosphate and the next three by GDP, which is suggestive of sequential GTP hydrolysis.

-	~~Authors~~:	+	Structure-based mechanism for activation of the AAA+ GTPase McrB by the endonuclease McrC.,Nirwan N, Itoh Y, Singh P, Bandyopadhyay S, Vinothkumar KR, Amunts A, Saikrishnan K Nat Commun. 2019 Jul 11;10(1):3058. doi: 10.1038/s41467-019-11084-1. PMID:31296862<ref>PMID:31296862</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6hz8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Amunts, A]]
		+	[[Category: Itoh, Y]]
		+	[[Category: Nirwan, N]]
		+	[[Category: Saikrishnan, K]]
		+	[[Category: Aaa+ superfamily]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Restriction enzyme]]

OCA: Protected "6hz8" [edit=sysop:move=sysop]

OCA — Wed, 31 Oct 2018 05:13:06 GMT

Protected "6hz8" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:13, 31 October 2018

OCA: New page: '''Unreleased structure''' The entry 6hz8 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 31 Oct 2018 05:13:03 GMT

New page: '''Unreleased structure''' The entry 6hz8 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6hz8 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]