6tqv - Revision history

OCA at 13:07, 24 January 2024

OCA — Wed, 24 Jan 2024 13:07:32 GMT

←Older revision		Revision as of 13:07, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6tqv' size='340' side='right'caption='[[6tqv]], [[Resolution\|resolution]] 1.35Å' scene=''>		<StructureSection load='6tqv' size='340' side='right'caption='[[6tqv]], [[Resolution\|resolution]] 1.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6tqv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bacillus_anthracis_(strain_sterne)~~ Bacillus anthracis ~~(strain sterne)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TQV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TQV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tqv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis_str._Sterne Bacillus anthracis str. Sterne]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TQV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TQV FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.3500097Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>nrdF, GBAA_1372 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~260799 Bacillus anthracis (strain Sterne)])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6tqv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tqv OCA], [https://pdbe.org/6tqv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tqv RCSB], [https://www.ebi.ac.uk/pdbsum/6tqv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tqv 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=6tqv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tqv OCA], [https://pdbe.org/6tqv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tqv RCSB], [https://www.ebi.ac.uk/pdbsum/6tqv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tqv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/Q81TB4_BACAN Q81TB4_BACAN]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.[PIRNR:PIRNR000355]	+	[https://www.uniprot.org/uniprot/Q81TB4_BACAN Q81TB4_BACAN] 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 6tqv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6tqv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonucleotide reductase 3D structures\|Ribonucleotide reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus anthracis str. Sterne]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Ribonucleoside-diphosphate reductase]]~~	+	[[Category: Grave K]]
-	[[Category: Grave, K]]	+	[[Category: Hogbom M]]
-	[[Category: Hogbom, M]]	+
-	~~[[Category: 2'-deoxyribonucleotide metabolism]]~~	+
-	~~[[Category: Dna replication]]~~	+
-	~~[[Category: Metal binding]]~~	+
-	~~[[Category: Oxidation reduction process]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 15:26, 8 June 2021

OCA — Tue, 08 Jun 2021 15:26:11 GMT

←Older revision		Revision as of 15:26, 8 June 2021
Line 3:		Line 3:
	<StructureSection load='6tqv' size='340' side='right'caption='[[6tqv]], [[Resolution\|resolution]] 1.35Å' scene=''>		<StructureSection load='6tqv' size='340' side='right'caption='[[6tqv]], [[Resolution\|resolution]] 1.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6tqv]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bacillus_anthracis_(strain_sterne) Bacillus anthracis (strain sterne)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TQV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6TQV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tqv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis_(strain_sterne) Bacillus anthracis (strain sterne)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TQV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TQV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nrdF, GBAA_1372 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=260799 Bacillus anthracis (strain Sterne)])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nrdF, GBAA_1372 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=260799 Bacillus anthracis (strain Sterne)])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </span></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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6tqv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tqv OCA], [~~http~~://pdbe.org/6tqv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6tqv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6tqv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6tqv 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=6tqv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tqv OCA], [https://pdbe.org/6tqv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tqv RCSB], [https://www.ebi.ac.uk/pdbsum/6tqv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tqv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/Q81TB4_BACAN Q81TB4_BACAN]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.[PIRNR:PIRNR000355]	+	[[https://www.uniprot.org/uniprot/Q81TB4_BACAN Q81TB4_BACAN]] 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 ==

OCA at 07:11, 29 April 2020

OCA — Wed, 29 Apr 2020 07:11:17 GMT

←Older revision		Revision as of 07:11, 29 April 2020
Line 1:		Line 1:

	==Crystal structure of ribonucleotide reductase NrdF from Bacillus anthracis aerobically soaked with Fe(II) and Mn(II) ions==		==Crystal structure of ribonucleotide reductase NrdF from Bacillus anthracis aerobically soaked with Fe(II) and Mn(II) ions==
-	<StructureSection load='6tqv' size='340' side='right'caption='[[6tqv]]' scene=''>	+	<StructureSection load='6tqv' size='340' side='right'caption='[[6tqv]], [[Resolution\|resolution]] 1.35Å' 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=6TQV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TQV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tqv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_anthracis_(strain_sterne) Bacillus anthracis (strain sterne)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TQV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TQV 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=6tqv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tqv OCA], [http://pdbe.org/6tqv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tqv RCSB], [http://www.ebi.ac.uk/pdbsum/6tqv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tqv 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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nrdF, GBAA_1372 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=260799 Bacillus anthracis (strain Sterne)])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://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'>[http://proteopedia.org/fgij/fg.htm?mol=6tqv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tqv OCA], [http://pdbe.org/6tqv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tqv RCSB], [http://www.ebi.ac.uk/pdbsum/6tqv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tqv ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q81TB4_BACAN Q81TB4_BACAN]] 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 ==
		+	Correct protein metallation in the complex mixture of the cell is a prerequisite for metalloprotein function. While some metals, such as Cu, are commonly chaperoned, specificity towards metals earlier in the Irving-Williams series is achieved through other means, the determinants of which are poorly understood. The dimetal carboxylate family of proteins provides an intriguing example, as different proteins, while sharing a common fold and the same 4-carboxylate 2-histidine coordination sphere, are known to require either a Fe/Fe, Mn/Fe or Mn/Mn cofactor for function. We previously showed that the R2lox proteins from this family spontaneously assemble the heterodinuclear Mn/Fe cofactor. Here we show that the class Ib ribonucleotide reductase R2 protein from Bacillus anthracis spontaneously assembles a Mn/Mn cofactor in vitro, under both aerobic and anoxic conditions, when the metal-free protein is subjected to incubation with Mn(II) and Fe(II) in equal concentrations. This observation provides an example of a protein scaffold intrinsically predisposed to defy the Irving-Williams series and supports the assumption that the Mn/Mn cofactor is the biologically relevant cofactor in vivo. Substitution of a second coordination sphere residue changes the spontaneous metallation of the protein to predominantly form a heterodinuclear Mn/Fe cofactor under aerobic conditions and a Mn/Mn metal center under anoxic conditions. Together, the results describe the intrinsic metal specificity of class Ib RNR and provide insight into control mechanisms for protein metallation.
		+
		+	The Bacillus anthracis class Ib ribonucleotide reductase subunit NrdF intrinsically selects manganese over iron.,Grave K, Griese JJ, Berggren G, Bennett MD, Hogbom M J Biol Inorg Chem. 2020 Apr 15. pii: 10.1007/s00775-020-01782-3. doi:, 10.1007/s00775-020-01782-3. PMID:32296998<ref>PMID:32296998</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6tqv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Grave K]]	+	[[Category: Ribonucleoside-diphosphate reductase]]
-	[[Category: Hogbom M]]	+	[[Category: Grave, K]]
		+	[[Category: Hogbom, M]]
		+	[[Category: 2'-deoxyribonucleotide metabolism]]
		+	[[Category: Dna replication]]
		+	[[Category: Metal binding]]
		+	[[Category: Oxidation reduction process]]
		+	[[Category: Oxidoreductase]]

OCA at 06:59, 15 April 2020

OCA — Wed, 15 Apr 2020 06:59:47 GMT

←Older revision		Revision as of 06:59, 15 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6tqv ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of ribonucleotide reductase NrdF from Bacillus anthracis aerobically soaked with Fe(II) and Mn(II) ions==
-		+	<StructureSection load='6tqv' size='340' side='right'caption='[[6tqv]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TQV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TQV 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=6tqv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tqv OCA], [http://pdbe.org/6tqv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tqv RCSB], [http://www.ebi.ac.uk/pdbsum/6tqv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tqv ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Grave K]]
		+	[[Category: Hogbom M]]

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

OCA — Wed, 25 Dec 2019 07:23:36 GMT

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

←Older revision

Revision as of 07:23, 25 December 2019

OCA: New page: '''Unreleased structure''' The entry 6tqv is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 25 Dec 2019 07:23:34 GMT

New page: '''Unreleased structure''' The entry 6tqv is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6tqv is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]