5udr

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Current revision (14:26, 6 March 2024) (edit) (undo)
 
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<StructureSection load='5udr' size='340' side='right'caption='[[5udr]], [[Resolution|resolution]] 2.62&Aring;' scene=''>
<StructureSection load='5udr' size='340' side='right'caption='[[5udr]], [[Resolution|resolution]] 2.62&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5udr]] 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=5UDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UDR FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5udr]] 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=5UDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UDR FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NMN:BETA-NICOTINAMIDE+RIBOSE+MONOPHOSPHATE'>NMN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.62&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5udq|5udq]], [[5udt|5udt]], [[5udu|5udu]], [[5udv|5udv]], [[5udw|5udw]], [[5udx|5udx]]</td></tr>
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<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=NMN:BETA-NICOTINAMIDE+RIBOSE+MONOPHOSPHATE'>NMN</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">A8P51_04975, IV39_GL000116, Nizo1839_0768, Nizo2891_3302, SRCM101060_01452 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1590 "Lactobacillus arabinosus" Fred et al.])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5udr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5udr OCA], [https://pdbe.org/5udr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5udr RCSB], [https://www.ebi.ac.uk/pdbsum/5udr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5udr ProSAT]</span></td></tr>
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<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=5udr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5udr OCA], [http://pdbe.org/5udr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5udr RCSB], [http://www.ebi.ac.uk/pdbsum/5udr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5udr ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[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>
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The lar operon in Lactobacillus plantarum encodes five Lar proteins (LarA/B/C/D/E) that collaboratively synthesize and incorporate a niacin-derived Ni-containing cofactor into LarA, an Ni-dependent lactate racemase. Previous studies have established that two molecules of LarE catalyze successive thiolation reactions by donating the sulfur atom of their exclusive cysteine residues to the substrate. However, the catalytic mechanism of this very unusual sulfur-sacrificing reaction remains elusive. In this work, we present the crystal structures of LarE in ligand-free and several ligand-bound forms, demonstrating that LarE is a member of the N-type ATP pyrophosphatase (PPase) family with a conserved N-terminal ATP PPase domain and a unique C-terminal domain harboring the putative catalytic site. Structural analysis, combined with structure-guided mutagenesis, leads us to propose a catalytic mechanism that establishes LarE as a paradigm for sulfur transfer through sacrificing its catalytic cysteine residue.
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Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE.,Fellner M, Desguin B, Hausinger RP, Hu J Proc Natl Acad Sci U S A. 2017 Aug 22;114(34):9074-9079. doi:, 10.1073/pnas.1704967114. Epub 2017 Aug 7. PMID:28784764<ref>PMID:28784764</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5udr" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Lactobacillus arabinosus fred et al]]
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[[Category: Lactiplantibacillus plantarum]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Desguin, B]]
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[[Category: Desguin B]]
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[[Category: Fellner, M]]
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[[Category: Fellner M]]
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[[Category: Hausinger, R P]]
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[[Category: Hausinger RP]]
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[[Category: Hu, J]]
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[[Category: Hu J]]
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[[Category: Ampylation]]
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[[Category: Atp pyrophophatase domain]]
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[[Category: Hexamer]]
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[[Category: Lactate]]
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[[Category: Lactate racemase]]
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[[Category: Lactate racemization]]
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[[Category: Lar]]
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[[Category: Lare]]
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[[Category: Pp-loop]]
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[[Category: Sulfur transferase]]
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[[Category: Transferase]]
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[[Category: Trimer]]
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Current revision

LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase in complex with nicotinamide mononucleotid NMN

PDB ID 5udr

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