5j3n - Revision history

OCA at 10:44, 6 September 2023

OCA — Wed, 06 Sep 2023 10:44:11 GMT

←Older revision		Revision as of 10:44, 6 September 2023
Line 1:		Line 1:

	==C-terminal domain of EcoR124I HsdR subunit fused with the pH-sensitive GFP variant ratiometric pHluorin==		==C-terminal domain of EcoR124I HsdR subunit fused with the pH-sensitive GFP variant ratiometric pHluorin==
-	<StructureSection load='5j3n' size='340' side='right' caption='[[5j3n]], [[Resolution\|resolution]] 2.45Å' scene=''>	+	<StructureSection load='5j3n' size='340' side='right'caption='[[5j3n]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j3n]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5J3N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j3n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria] and [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J3N FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non~~-~~Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=GYS:[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYS</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]] 2.45Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hsdR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GYS:[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYS</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=5j3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3n OCA], [~~http~~://pdbe.org/5j3n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5j3n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5j3n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3n 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=5j3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3n OCA], [https://pdbe.org/5j3n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j3n RCSB], [https://www.ebi.ac.uk/pdbsum/5j3n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.	+	[https://www.uniprot.org/uniprot/T1R1_ECOLX T1R1_ECOLX] The restriction (R) subunit of a type I restriction enzyme that recognizes 5'-GAAN(7)RTCG-3' and cleaves a random distance away. Subunit R is required for both nuclease and ATPase activities, but not for modification (Probable) (PubMed:12654995). After locating an unmethylated recognition site, the enzyme complex serves as a molecular motor that translocates DNA in an ATP-dependent manner until a collision occurs that triggers cleavage (Probable). The enzyme undergoes major structural changes to bring the motor domains into contact with DNA, allowing DNA translocation. This prevents DNA access to the catalytic domains of both the R and M subunits, preventing both restriction and methylation (PubMed:32483229).<ref>PMID:32483229</ref> <ref>PMID:12654995</ref> <ref>PMID:2784505</ref> <ref>PMID:32483229</ref> [https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:

	==See Also==		==See Also==
-	*[[Green Fluorescent Protein\|Green Fluorescent Protein]]	+	*[[Green Fluorescent Protein 3D structures\|Green Fluorescent Protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus coli migula 1895~~]]	+	[[Category: Aequorea victoria]]
-	[[Category: ~~Ettrich, R~~]]	+	[[Category: Escherichia coli]]
-	[[Category: ~~Grinkevich, P~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Iermak, I~~]]	+	[[Category: Ettrich R]]
-	[[Category: ~~Ludwig, J~~]]	+	[[Category: Grinkevich P]]
-	[[Category: ~~Luedtke, N~~]]	+	[[Category: Iermak I]]
-	[[Category: ~~Mesters,~~ J R]]	+	[[Category: Ludwig J]]
-	[[Category: ~~Ecor124i~~]]	+	[[Category: Luedtke N]]
-	[[Category: ~~Fusion protein]]~~	+	[[Category: Mesters JR]]
-	~~[[Category: Gfp]]~~	+
-	~~[[Category: Hsdr]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Phluorin]]~~	+
-	~~[[Category: Type i restriction-modification system~~]]	+

OCA at 06:23, 22 August 2018

OCA — Wed, 22 Aug 2018 06:23:51 GMT

←Older revision		Revision as of 06:23, 22 August 2018
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.		[[http://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Although EcoR124 is one of the better-studied Type I restriction-modification enzymes, it still presents many challenges to detailed analyses because of its structural and functional complexity and missing structural information. In all available structures of its motor subunit HsdR, responsible for DNA translocation and cleavage, a large part of the HsdR C terminus remains unresolved. The crystal structure of the C terminus of HsdR, obtained with a crystallization chaperone in the form of pHluorin fusion and refined to 2.45 A, revealed that this part of the protein forms an independent domain with its own hydrophobic core and displays a unique alpha-helical fold. The full-length HsdR model, based on the wild-type structure and the herein determined C-terminal domain, disclosed a proposed DNA-binding groove lined by positively charged residues. In vivo and in vitro assays with a C-terminal deletion mutant of HsdR supported the idea that this domain is involved in complex assembly and DNA binding. Conserved residues identified through sequence analysis of the C-terminal domain may play a key role in protein-protein and protein-DNA interactions. We conclude that the motor subunit of EcoR124 comprises five structural and functional domains, with the fifth, C-terminal domain revealing a unique fold characterized by four conserved motifs in the IC subfamily of Type I restriction-modification systems. In summary, structural and biochemical results reported here support a model in which the C-terminal domain of the motor subunit HsdR of the endonuclease EcoR124 is involved in complex assembly and DNA binding.
		+
		+	Crystal structure of a novel domain of the motor subunit of the Type I restriction enzyme EcoR124 involved in complex assembly and DNA binding.,Grinkevich P, Sinha D, Iermak I, Guzanova A, Weiserova M, Ludwig J, Mesters JR, Ettrich RH J Biol Chem. 2018 Jul 27. pii: RA118.003978. doi: 10.1074/jbc.RA118.003978. PMID:30054276<ref>PMID:30054276</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5j3n" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Green Fluorescent Protein\|Green Fluorescent Protein]]		*[[Green Fluorescent Protein\|Green Fluorescent Protein]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:07, 8 March 2018

OCA — Thu, 08 Mar 2018 06:07:03 GMT

←Older revision		Revision as of 06:07, 8 March 2018
Line 3:		Line 3:
	<StructureSection load='5j3n' size='340' side='right' caption='[[5j3n]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='5j3n' size='340' side='right' caption='[[5j3n]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j3n]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J3N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j3n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J3N FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GYS:[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYS</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GYS:[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYS</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hsdR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=5j3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3n OCA], [http://pdbe.org/5j3n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j3n RCSB], [http://www.ebi.ac.uk/pdbsum/5j3n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3n 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=5j3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3n OCA], [http://pdbe.org/5j3n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j3n RCSB], [http://www.ebi.ac.uk/pdbsum/5j3n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.		[[http://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
		+
		+	==See Also==
		+	*[[Green Fluorescent Protein\|Green Fluorescent Protein]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Ettrich, R]]		[[Category: Ettrich, R]]
	[[Category: Grinkevich, P]]		[[Category: Grinkevich, P]]

OCA at 11:42, 12 April 2017

OCA — Wed, 12 Apr 2017 11:42:09 GMT

←Older revision		Revision as of 11:42, 12 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5j3n is ~~ON HOLD until Paper Publication~~	+	==C-terminal domain of EcoR124I HsdR subunit fused with the pH-sensitive GFP variant ratiometric pHluorin==
-		+	<StructureSection load='5j3n' size='340' side='right' caption='[[5j3n]], [[Resolution\|resolution]] 2.45Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5j3n]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J3N FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GYS:[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYS</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=5j3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3n OCA], [http://pdbe.org/5j3n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j3n RCSB], [http://www.ebi.ac.uk/pdbsum/5j3n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3n ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ettrich, R]]
		+	[[Category: Grinkevich, P]]
		+	[[Category: Iermak, I]]
		+	[[Category: Ludwig, J]]
		+	[[Category: Luedtke, N]]
		+	[[Category: Mesters, J R]]
		+	[[Category: Ecor124i]]
		+	[[Category: Fusion protein]]
		+	[[Category: Gfp]]
		+	[[Category: Hsdr]]
		+	[[Category: Hydrolase]]
		+	[[Category: Phluorin]]
		+	[[Category: Type i restriction-modification system]]

OCA at 15:01, 15 May 2016

OCA — Sun, 15 May 2016 15:01:21 GMT

←Older revision		Revision as of 15:01, 15 May 2016
Line 3:		Line 3:
	The entry 5j3n is ON HOLD until Paper Publication		The entry 5j3n is ON HOLD until Paper Publication

-	Authors: ~~Grinkevich, P., Iermak, I., Luedtke, N., Mesters, J.R., Ettrich, R., Ludwig, J.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Luedtke, N]]
-	[[Category: Iermak, I]]
-	[[Category: Grinkevich, P]]
-	[[Category: Mesters, J.R]]
-	[[Category: Ettrich, R]]
-	[[Category: Ludwig, J]]

OCA: Protected "5j3n" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 01:23:55 GMT

Protected "5j3n" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:23, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5j3n is ON HOLD until Paper Publication Authors: Grinkevich, P., Iermak, I., Luedtke, N., Mesters, J.R., Ettrich, R., Ludwig, J. Description: [[Ca...

OCA — Wed, 11 May 2016 01:23:53 GMT

New page: '''Unreleased structure''' The entry 5j3n is ON HOLD until Paper Publication Authors: Grinkevich, P., Iermak, I., Luedtke, N., Mesters, J.R., Ettrich, R., Ludwig, J. Description: [[Ca...

New page

'''Unreleased structure'''

The entry 5j3n is ON HOLD until Paper Publication

Authors: Grinkevich, P., Iermak, I., Luedtke, N., Mesters, J.R., Ettrich, R., Ludwig, J.

Description:
[[Category: Unreleased Structures]]
[[Category: Luedtke, N]]
[[Category: Iermak, I]]
[[Category: Grinkevich, P]]
[[Category: Mesters, J.R]]
[[Category: Ettrich, R]]
[[Category: Ludwig, J]]