5zmm - Revision history

OCA at 10:28, 27 March 2024

2024-03-27T10:28:26Z

←Older revision		Revision as of 10:28, 27 March 2024
Line 1:		Line 1:

	==Structure of the Type IV phosphorothioation-dependent restriction endonuclease ScoMcrA==		==Structure of the Type IV phosphorothioation-dependent restriction endonuclease ScoMcrA==
-	<StructureSection load='5zmm' size='340' side='right' caption='[[5zmm]], [[Resolution\|resolution]] 3.15Å' scene=''>	+	<StructureSection load='5zmm' size='340' side='right'caption='[[5zmm]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zmm]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Strco Strco~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZMM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZMM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zmm]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_coelicolor_A3(2) Streptomyces coelicolor A3(2)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZMM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZMM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=SO4:SULFATE+ION'>SO4</scene~~>, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3.15Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~SCO4631 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=100226 STRCO])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5zmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zmm OCA], [~~http~~://pdbe.org/5zmm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zmm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zmm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zmm 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=5zmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zmm OCA], [https://pdbe.org/5zmm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zmm RCSB], [https://www.ebi.ac.uk/pdbsum/5zmm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zmm ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q9L0M9_STRCO Q9L0M9_STRCO]
-	There have been very few reports on protein domains that specifically recognize sulfur. Here we present the crystal structure of the sulfur-binding domain (SBD) from the DNA phosphorothioation (PT)-dependent restriction endonuclease ScoMcrA. SBD contains a hydrophobic surface cavity that is formed by the aromatic ring of Y164, the pyrolidine ring of P165, and the non-polar side chains of four other residues that serve as lid, base, and wall of the cavity. The SBD and PT-DNA undergo conformational changes upon binding. The S(187)RGRR(191) loop inserts into the DNA major groove to make contacts with the bases of the GPSGCC core sequence. Mutating key residues of SBD impairs PT-DNA association. More than 1000 sequenced microbial species from fourteen phyla contain SBD homologs. We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo. These results show that SBD-like PT-DNA readers exist widely in prokaryotes.	+
-		+
-	~~Structural basis for the recognition of sulfur in phosphorothioated DNA.,Liu G, Fu W, Zhang Z, He Y, Yu H, Wang Y, Wang X, Zhao YL, Deng Z, Wu G, He X Nat Commun. 2018 Nov 8;9(1)~~:~~4689. doi: 10.1038~~/~~s41467-018-07093-1. PMID:30409991<ref>PMID:30409991<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5zmm" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Strco~~]]	+	[[Category: Large Structures]]
-	[[Category: Deng, Z]]	+	[[Category: Deng Z]]
-	[[Category: Fu, W]]	+	[[Category: Fu W]]
-	[[Category: He, X]]	+	[[Category: He X]]
-	[[Category: He, Y]]	+	[[Category: He Y]]
-	[[Category: Liu, G]]	+	[[Category: Liu G]]
-	[[Category: Wu, G]]	+	[[Category: Wu G]]
-	[[Category: Yu, H]]	+	[[Category: Yu H]]
-	[[Category: Zhang, Z]]	+	[[Category: Zhang Z]]
-	[[Category: Zhao, Y]]	+	[[Category: Zhao Y]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Dna phosphorothioation]]~~	+
-	~~[[Category: Type iv restriction endonuclease~~]]	+

OCA at 20:51, 2 December 2018

2018-12-02T20:51:19Z

←Older revision		Revision as of 20:51, 2 December 2018
Line 3:		Line 3:
	<StructureSection load='5zmm' size='340' side='right' caption='[[5zmm]], [[Resolution\|resolution]] 3.15Å' scene=''>		<StructureSection load='5zmm' size='340' side='right' caption='[[5zmm]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zmm]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZMM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZMM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zmm]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Strco Strco]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZMM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZMM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SCO4631 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=100226 STRCO])</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=5zmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zmm OCA], [http://pdbe.org/5zmm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zmm RCSB], [http://www.ebi.ac.uk/pdbsum/5zmm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zmm 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=5zmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zmm OCA], [http://pdbe.org/5zmm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zmm RCSB], [http://www.ebi.ac.uk/pdbsum/5zmm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zmm ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	There have been very few reports on protein domains that specifically recognize sulfur. Here we present the crystal structure of the sulfur-binding domain (SBD) from the DNA phosphorothioation (PT)-dependent restriction endonuclease ScoMcrA. SBD contains a hydrophobic surface cavity that is formed by the aromatic ring of Y164, the pyrolidine ring of P165, and the non-polar side chains of four other residues that serve as lid, base, and wall of the cavity. The SBD and PT-DNA undergo conformational changes upon binding. The S(187)RGRR(191) loop inserts into the DNA major groove to make contacts with the bases of the GPSGCC core sequence. Mutating key residues of SBD impairs PT-DNA association. More than 1000 sequenced microbial species from fourteen phyla contain SBD homologs. We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo. These results show that SBD-like PT-DNA readers exist widely in prokaryotes.
		+
		+	Structural basis for the recognition of sulfur in phosphorothioated DNA.,Liu G, Fu W, Zhang Z, He Y, Yu H, Wang Y, Wang X, Zhao YL, Deng Z, Wu G, He X Nat Commun. 2018 Nov 8;9(1):4689. doi: 10.1038/s41467-018-07093-1. PMID:30409991<ref>PMID:30409991</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5zmm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Strco]]
	[[Category: Deng, Z]]		[[Category: Deng, Z]]
	[[Category: Fu, W]]		[[Category: Fu, W]]

OCA at 07:57, 26 September 2018

2018-09-26T07:57:45Z

←Older revision		Revision as of 07:57, 26 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zmm ~~is ON HOLD~~	+	==Structure of the Type IV phosphorothioation-dependent restriction endonuclease ScoMcrA==
-		+	<StructureSection load='5zmm' size='340' side='right' caption='[[5zmm]], [[Resolution\|resolution]] 3.15Å' scene=''>
-	~~Authors~~: ~~Liu, G~~., ~~Fu, W~~.~~, Zhang, Z~~., He, Y., ~~Yu, H~~., ~~Zhao, Y~~., Deng, Z~~., Wu, G.~~, He, X.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5zmm]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZMM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZMM FirstGlance]. <br>
-	~~Description~~: ~~An unprecedented recognition mechanism of sulfur in phosphorothioated DNA~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5zmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zmm OCA], [http://pdbe.org/5zmm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zmm RCSB], [http://www.ebi.ac.uk/pdbsum/5zmm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zmm ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Deng, Z]]
		+	[[Category: Fu, W]]
		+	[[Category: He, X]]
		+	[[Category: He, Y]]
		+	[[Category: Liu, G]]
		+	[[Category: Wu, G]]
	[[Category: Yu, H]]		[[Category: Yu, H]]
-	[[Category: Wu, G]]
-	[[Category: He, X]]
	[[Category: Zhang, Z]]		[[Category: Zhang, Z]]
-	[[Category: Fu, W]]
	[[Category: Zhao, Y]]		[[Category: Zhao, Y]]
-	[[Category: ~~He, Y~~]]	+	[[Category: Dna binding protein]]
-	[[Category: ~~Deng, Z~~]]	+	[[Category: Dna phosphorothioation]]
-	[[Category: ~~Liu, G~~]]	+	[[Category: Type iv restriction endonuclease]]

OCA at 04:03, 18 April 2018

2018-04-18T04:03:39Z

←Older revision		Revision as of 04:03, 18 April 2018
Line 3:		Line 3:
	The entry 5zmm is ON HOLD		The entry 5zmm is ON HOLD

-	Authors: ~~LIU~~, G., FU, W., ~~ZHANG~~, Z., HE, Y., YU, H., ~~ZHAO~~, Y., ~~DENG~~, Z., WU, G., HE, X.	+	Authors: Liu, G., Fu, W., Zhang, Z., He, Y., Yu, H., Zhao, Y., Deng, Z., Wu, G., He, X.

	Description: An unprecedented recognition mechanism of sulfur in phosphorothioated DNA		Description: An unprecedented recognition mechanism of sulfur in phosphorothioated DNA

OCA: Protected "5zmm" [edit=sysop:move=sysop]

2018-04-11T12:21:56Z

Protected "5zmm" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:21, 11 April 2018

OCA: New page: '''Unreleased structure''' The entry 5zmm is ON HOLD Authors: LIU, G., FU, W., ZHANG, Z., HE, Y., YU, H., ZHAO, Y., DENG, Z., WU, G., HE, X. Description: An unprecedented recognition m...

2018-04-11T12:21:55Z

New page: '''Unreleased structure''' The entry 5zmm is ON HOLD Authors: LIU, G., FU, W., ZHANG, Z., HE, Y., YU, H., ZHAO, Y., DENG, Z., WU, G., HE, X. Description: An unprecedented recognition m...

New page

'''Unreleased structure'''

The entry 5zmm is ON HOLD

Authors: LIU, G., FU, W., ZHANG, Z., HE, Y., YU, H., ZHAO, Y., DENG, Z., WU, G., HE, X.

Description: An unprecedented recognition mechanism of sulfur in phosphorothioated DNA
[[Category: Unreleased Structures]]
[[Category: Yu, H]]
[[Category: Wu, G]]
[[Category: He, X]]
[[Category: Zhang, Z]]
[[Category: Fu, W]]
[[Category: Zhao, Y]]
[[Category: He, Y]]
[[Category: Deng, Z]]
[[Category: Liu, G]]