6utp - Revision history

OCA at 07:58, 11 October 2023

OCA — Wed, 11 Oct 2023 07:58:03 GMT

←Older revision		Revision as of 07:58, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6utp' size='340' side='right'caption='[[6utp]], [[Resolution\|resolution]] 3.55Å' scene=''>		<StructureSection load='6utp' size='340' side='right'caption='[[6utp]], [[Resolution\|resolution]] 3.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6utp]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"lactobacillus_arabinosus"_fred_et_al. "lactobacillus arabinosus" fred et al.~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UTP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6UTP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6utp]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactiplantibacillus_plantarum Lactiplantibacillus plantarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UTP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UTP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 3.55Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">larE, AVR82_02840, BIZ32_00440, CFM86_00460, CUR48_11145, E3O64_03880, IV39_GL000116, LPJSA22_00116, LpLQ80_00490, Nizo1839_0768, Nizo2891_3302 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1590 "Lactobacillus arabinosus" Fred et al.])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=6utp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6utp OCA], [~~http~~://pdbe.org/6utp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6utp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6utp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6utp 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=6utp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6utp OCA], [https://pdbe.org/6utp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6utp RCSB], [https://www.ebi.ac.uk/pdbsum/6utp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6utp ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/LARE_LACPL LARE_LACPL] Involved in the biosynthesis of a nickel-pincer cofactor ((SCS)Ni(II) pincer complex). Catalyzes the ATP-dependent incorporation of two sulfur atoms in pyridinium-3,5-biscarboxylic acid mononucleotide (P2CMN) to yield pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN). The source of sulfur is the enzyme itself: Cys-176 of LarE is the sulfur donor, thereby being converted into dehydroalanine, and is not regenerated in vivo. Thus, two molecules of LarE undergo sacrificial sulfur transfer to create one P2TMN (PubMed:27114550). Binds nickel (PubMed:24710389). Is required for the activation of the lactate racemase LarA (PubMed:24710389). May also be involved in the activation of other nickel-pincer cofactor-dependent enzymes (PubMed:27114550).<ref>PMID:24710389</ref> <ref>PMID:27114550</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lactobacillus arabinosus fred et al~~]]	+	[[Category: Lactiplantibacillus plantarum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fellner, M]]	+	[[Category: Fellner M]]
-	[[Category: Hausinger~~, R P~~]]	+	[[Category: Hausinger RP]]
-	[[Category: Hu, J]]	+	[[Category: Hu J]]
-	[[Category: Huizenga, K]]	+	[[Category: Huizenga K]]
-	~~[[Category: Ampylation]]~~	+
-	~~[[Category: Atp pyrophophatase domain]]~~	+
-	~~[[Category: Lactate racemase]]~~	+
-	~~[[Category: Lactate racemization]]~~	+
-	~~[[Category: Lar]]~~	+
-	~~[[Category: Pp-loop]]~~	+
-	~~[[Category: Sulfur transferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:19, 15 April 2020

OCA — Wed, 15 Apr 2020 07:19:33 GMT

←Older revision		Revision as of 07:19, 15 April 2020
Line 3:		Line 3:
	<StructureSection load='6utp' size='340' side='right'caption='[[6utp]], [[Resolution\|resolution]] 3.55Å' scene=''>		<StructureSection load='6utp' size='340' side='right'caption='[[6utp]], [[Resolution\|resolution]] 3.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6utp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"lactobacillus_arabinosus"_fred_et_al. "lactobacillus arabinosus" fred et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UTP OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6UTP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6utp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"lactobacillus_arabinosus"_fred_et_al. "lactobacillus arabinosus" fred et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UTP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6UTP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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">larE, AVR82_02840, BIZ32_00440, CFM86_00460, CUR48_11145, E3O64_03880, IV39_GL000116, LPJSA22_00116, LpLQ80_00490, Nizo1839_0768, Nizo2891_3302 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1590 "Lactobacillus arabinosus" Fred et al.])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">larE, AVR82_02840, BIZ32_00440, CFM86_00460, CUR48_11145, E3O64_03880, IV39_GL000116, LPJSA22_00116, LpLQ80_00490, Nizo1839_0768, Nizo2891_3302 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1590 "Lactobacillus arabinosus" Fred et al.])</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=6utp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6utp OCA], [http://pdbe.org/6utp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6utp RCSB], [http://www.ebi.ac.uk/pdbsum/6utp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6utp 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=6utp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6utp OCA], [http://pdbe.org/6utp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6utp RCSB], [http://www.ebi.ac.uk/pdbsum/6utp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6utp ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Detailed crystallographic characterization of a tri-aspartate metal-binding site previously identified on the three-fold symmetry axis of a hexameric enzyme, LarE from Lactobacillus plantarum, was conducted. By screening an array of monovalent, divalent, and trivalent metal ions, we demonstrated that this metal binding site stoichiometrically binds Ca(2+), Mn(2+), Fe(2+)/Fe(3+), Co(2+), Ni(2+), Cu(2+), Zn(2+), and Cd(2+), but not monovalent metal ions, Cr(3+), Mg(2+), Y(3+), Sr(2+) or Ba(2+). Extensive database searches resulted in only 13 similar metal binding sites in other proteins, indicative of the rareness of tri-aspartate architectures, which allows for engineering such a selective multivalent metal ion binding site into target macromolecules for structural and biophysical characterization.
		+
		+	Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE.,Fellner M, Huizenga KG, Hausinger RP, Hu J Sci Rep. 2020 Apr 2;10(1):5830. doi: 10.1038/s41598-020-62847-6. PMID:32242052<ref>PMID:32242052</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6utp" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 18:02, 20 November 2019

OCA — Wed, 20 Nov 2019 18:02:09 GMT

←Older revision		Revision as of 18:02, 20 November 2019
Line 3:		Line 3:
	<StructureSection load='6utp' size='340' side='right'caption='[[6utp]], [[Resolution\|resolution]] 3.55Å' scene=''>		<StructureSection load='6utp' size='340' side='right'caption='[[6utp]], [[Resolution\|resolution]] 3.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6utp]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UTP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UTP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6utp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"lactobacillus_arabinosus"_fred_et_al. "lactobacillus arabinosus" fred et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UTP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UTP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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">larE, AVR82_02840, BIZ32_00440, CFM86_00460, CUR48_11145, E3O64_03880, IV39_GL000116, LPJSA22_00116, LpLQ80_00490, Nizo1839_0768, Nizo2891_3302 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1590 "Lactobacillus arabinosus" Fred et al.])</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=6utp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6utp OCA], [http://pdbe.org/6utp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6utp RCSB], [http://www.ebi.ac.uk/pdbsum/6utp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6utp 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=6utp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6utp OCA], [http://pdbe.org/6utp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6utp RCSB], [http://www.ebi.ac.uk/pdbsum/6utp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6utp ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lactobacillus arabinosus fred et al]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Fellner, M]]		[[Category: Fellner, M]]

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

OCA — Wed, 06 Nov 2019 06:58:10 GMT

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

←Older revision

Revision as of 06:58, 6 November 2019

OCA: New page: ==LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase in complex with cobalt== == Structural highlights ==
<table><tr><td colspan='2'>[[6utp]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UTP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UTP FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6utp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6utp OCA], [http://pdbe.org/6utp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6utp RCSB], [http://www.ebi.ac.uk/pdbsum/6utp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6utp ProSAT]</span></td></tr>
</table>
TOC
</StructureSection>
[[Category: Large Structures]]
[[Category: Fellner, M]]
[[Category: Hausinger, R P]]
[[Category: Hu, J]]
[[Category: Huizenga, K]]
[[Category: Ampylation]]
[[Category: Atp pyrophophatase domain]]
[[Category: Lactate racemase]]
[[Category: Lactate racemization]]
[[Category: Lar]]
[[Category: Pp-loop]]
[[Category: Sulfur transferase]]
[[Category: Transferase]]