6zjk - Revision history

OCA at 11:53, 1 February 2024

OCA — Thu, 01 Feb 2024 11:53:29 GMT

←Older revision		Revision as of 11:53, 1 February 2024
Line 3:		Line 3:
	<StructureSection load='6zjk' size='340' side='right'caption='[[6zjk]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6zjk' size='340' side='right'caption='[[6zjk]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6zjk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Clobm Clobm~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZJK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zjk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_botulinum_A3_str._Loch_Maree Clostridium botulinum A3 str. Loch Maree]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZJK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>nrdB, CLK_2200 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~498214 CLOBM])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1]~~ </~~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=6zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zjk OCA], [https://pdbe.org/6zjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zjk RCSB], [https://www.ebi.ac.uk/pdbsum/6zjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zjk 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=6zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zjk OCA], [https://pdbe.org/6zjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zjk RCSB], [https://www.ebi.ac.uk/pdbsum/6zjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zjk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/B1KYY8_CLOBM B1KYY8_CLOBM]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.[PIRNR:PIRNR000355]	+	[https://www.uniprot.org/uniprot/B1KYY8_CLOBM B1KYY8_CLOBM] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.[PIRNR:PIRNR000355]
	<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 6zjk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6zjk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonucleotide reductase 3D structures\|Ribonucleotide reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Clobm~~]]	+	[[Category: Clostridium botulinum A3 str. Loch Maree]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Ribonucleoside-diphosphate reductase]]~~	+	[[Category: Martinez-Carranza M]]
-	[[Category: Martinez-Carranza, M]]	+	[[Category: Stenmark P]]
-	[[Category: Stenmark, P]]	+
-	~~[[Category: Metal binding protein]]~~	+
-	~~[[Category: Nucleotide]]~~	+
-	~~[[Category: R2]]~~	+
-	~~[[Category: Reductase]]~~	+
-	~~[[Category: Ribonucleotide~~]]	+

OCA at 06:55, 14 April 2021

OCA — Wed, 14 Apr 2021 06:55:02 GMT

←Older revision		Revision as of 06:55, 14 April 2021
Line 1:		Line 1:

	==Ribonucleotide reductase R2 subunit from Clostridium botulinum==		==Ribonucleotide reductase R2 subunit from Clostridium botulinum==
-	<StructureSection load='6zjk' size='340' side='right'caption='[[6zjk]]' scene=''>	+	<StructureSection load='6zjk' size='340' side='right'caption='[[6zjk]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZJK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6ZJK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zjk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Clobm Clobm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZJK FirstGlance]. <br>
-	</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=6zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zjk OCA], [~~http~~://pdbe.org/6zjk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6zjk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6zjk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6zjk ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nrdB, CLK_2200 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=498214 CLOBM])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </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=6zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zjk OCA], [https://pdbe.org/6zjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zjk RCSB], [https://www.ebi.ac.uk/pdbsum/6zjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zjk ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/B1KYY8_CLOBM B1KYY8_CLOBM]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.[PIRNR:PIRNR000355]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ribonucleotide reductase (RNR) is a central enzyme for the synthesis of DNA building blocks. Most aerobic organisms, including nearly all eukaryotes, have class I RNRs consisting of R1 and R2 subunits. The catalytic R1 subunit contains an overall activity site that can allosterically turn the enzyme on or off by the binding of ATP or dATP, respectively. The mechanism behind the ability to turn the enzyme off via the R1 subunit involves the formation of different types of R1 oligomers in most studied species and R1-R2 octamers in Escherichia coli To better understand the distribution of different oligomerization mechanisms, we characterized the enzyme from Clostridium botulinum, which belongs to a subclass of class I RNRs not studied before. The recombinantly expressed enzyme was analyzed by size-exclusion chromatography, gas-phase electrophoretic mobility macromolecular analysis, EM, X-ray crystallography, and enzyme assays. Interestingly, it shares the ability of the E. coli RNR to form inhibited R1-R2 octamers in the presence of dATP but, unlike the E. coli enzyme, cannot be turned off by combinations of ATP and dGTP/dTTP. A phylogenetic analysis of class I RNRs suggests that activity regulation is not ancestral but was gained after the first subclasses diverged and that RNR subclasses with inhibition mechanisms involving R1 oligomerization belong to a clade separated from the two subclasses forming R1-R2 octamers. These results give further insight into activity regulation in class I RNRs as an evolutionarily dynamic process.
		+
		+	A ribonucleotide reductase from Clostridium botulinum reveals distinct evolutionary pathways to regulation via the overall activity site.,Martinez-Carranza M, Jonna VR, Lundin D, Sahlin M, Carlson LA, Jemal N, Hogbom M, Sjoberg BM, Stenmark P, Hofer A J Biol Chem. 2020 Nov 13;295(46):15576-15587. doi: 10.1074/jbc.RA120.014895. Epub, 2020 Sep 3. PMID:32883811<ref>PMID:32883811</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6zjk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Clobm]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Martinez-Carranza M]]	+	[[Category: Ribonucleoside-diphosphate reductase]]
-	[[Category: Stenmark P]]	+	[[Category: Martinez-Carranza, M]]
		+	[[Category: Stenmark, P]]
		+	[[Category: Metal binding protein]]
		+	[[Category: Nucleotide]]
		+	[[Category: R2]]
		+	[[Category: Reductase]]
		+	[[Category: Ribonucleotide]]

OCA at 07:12, 30 September 2020

OCA — Wed, 30 Sep 2020 07:12:34 GMT

←Older revision		Revision as of 07:12, 30 September 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6zjk ~~is ON HOLD until Paper Publication~~	+	==Ribonucleotide reductase R2 subunit from Clostridium botulinum==
-		+	<StructureSection load='6zjk' size='340' side='right'caption='[[6zjk]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZJK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZJK FirstGlance]. <br>
-	~~Description~~:	+	</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=6zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zjk OCA], [http://pdbe.org/6zjk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zjk RCSB], [http://www.ebi.ac.uk/pdbsum/6zjk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zjk ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Martinez-Carranza M]]
		+	[[Category: Stenmark P]]

OCA at 09:29, 29 July 2020

OCA — Wed, 29 Jul 2020 09:29:50 GMT

←Older revision		Revision as of 09:29, 29 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 08 Jul 2020 11:14:02 GMT

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

←Older revision

Revision as of 11:14, 8 July 2020

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

OCA — Wed, 08 Jul 2020 11:14:00 GMT

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

New page

'''Unreleased structure'''

The entry 6zjk is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]