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| | <StructureSection load='6bwq' size='340' side='right'caption='[[6bwq]], [[Resolution|resolution]] 1.85Å' scene=''> | | <StructureSection load='6bwq' size='340' side='right'caption='[[6bwq]], [[Resolution|resolution]] 1.85Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6bwq]] is a 2 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=6BWQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BWQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6bwq]] is a 2 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=6BWQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BWQ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CTP:CYTIDINE-5-TRIPHOSPHATE'>CTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 1.85Å</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=6bwq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bwq OCA], [http://pdbe.org/6bwq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bwq RCSB], [http://www.ebi.ac.uk/pdbsum/6bwq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bwq ProSAT]</span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CTP:CYTIDINE-5-TRIPHOSPHATE'>CTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=6bwq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bwq OCA], [https://pdbe.org/6bwq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bwq RCSB], [https://www.ebi.ac.uk/pdbsum/6bwq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bwq ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/LARC_LACPL LARC_LACPL]] Involved in the biosynthesis of a nickel-pincer cofactor ((SCS)Ni(II) pincer complex). Binds Ni(2+), and functions in nickel delivery to pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN), to form the mature cofactor. Is required for the activation of the lactate racemase LarA. May also be involved in the activation of other nickel-pincer cofactor-dependent enzymes.<ref>PMID:24710389</ref> <ref>PMID:27114550</ref> | + | [https://www.uniprot.org/uniprot/LARC_LACPL LARC_LACPL] Involved in the biosynthesis of a nickel-pincer cofactor ((SCS)Ni(II) pincer complex). Binds Ni(2+), and functions in nickel delivery to pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN), to form the mature cofactor. Is required for the activation of the lactate racemase LarA. May also be involved in the activation of other nickel-pincer cofactor-dependent enzymes.<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 == |
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| | __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: Ctp]]
| + | |
| - | [[Category: Hexamer]]
| + | |
| - | [[Category: Lactate]]
| + | |
| - | [[Category: Lactate racemase]]
| + | |
| - | [[Category: Lactate racemization]]
| + | |
| - | [[Category: Lar]]
| + | |
| - | [[Category: Larc]]
| + | |
| - | [[Category: Metal binding protein]]
| + | |
| - | [[Category: Nickel]]
| + | |
| - | [[Category: Nickel transferase]]
| + | |
| - | [[Category: Trimer]]
| + | |
| Structural highlights
Function
LARC_LACPL Involved in the biosynthesis of a nickel-pincer cofactor ((SCS)Ni(II) pincer complex). Binds Ni(2+), and functions in nickel delivery to pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN), to form the mature cofactor. Is required for the activation of the lactate racemase LarA. May also be involved in the activation of other nickel-pincer cofactor-dependent enzymes.[1] [2]
Publication Abstract from PubMed
Bacterial lactate racemase is a nickel-dependent enzyme that contains a cofactor, nickel pyridinium-3,5-bisthiocarboxylic acid mononucleotide, hereafter named nickel-pincer nucleotide (NPN). The LarC enzyme from the bacterium Lactobacillus plantarum participates in NPN biosynthesis by inserting nickel ion into pyridinium-3,5-bisthiocarboxylic acid mononucleotide,. This reaction, known in organometallic chemistry as a cyclometalation, is characterized by the formation of new metal-carbon and metal-sulfur sigma bonds. LarC is therefore the first cyclometallase identified in nature, but the molecular mechanism of LarC-catalyzed cylometalation is unknown. Here, we show that LarC activity requires Mn(2+)-dependent CTP hydrolysis. The crystal structure of the C-terminal domain of LarC at 1.85 A resolution revealed a hexameric ferredoxin-like fold and an unprecedented CTP binding pocket. The loss of function of LarC variants with alanine variants of acidic residues lead us to propose a carboxylate-assisted mechanism for nickel insertion. This works also demonstrates the in vitro synthesis and purification of the NPN cofactor, opening new opportunities for the study of this intriguing cofactor and of NPN-utilizing enzymes.
Biosynthesis of the nickel-pincer nucleotide cofactor of lactate racemase requires a CTP-dependent cyclometallase.,Desguin B, Fellner M, Riant O, Hu J, Hausinger R, Hols P, Soumillion P J Biol Chem. 2018 Jun 10. pii: RA118.003741. doi: 10.1074/jbc.RA118.003741. PMID:29887527[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Desguin B, Goffin P, Viaene E, Kleerebezem M, Martin-Diaconescu V, Maroney MJ, Declercq JP, Soumillion P, Hols P. Lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system. Nat Commun. 2014 Apr 7;5:3615. doi: 10.1038/ncomms4615. PMID:24710389 doi:http://dx.doi.org/10.1038/ncomms4615
- ↑ Desguin B, Soumillion P, Hols P, Hausinger RP. Nickel-pincer cofactor biosynthesis involves LarB-catalyzed pyridinium carboxylation and LarE-dependent sacrificial sulfur insertion. Proc Natl Acad Sci U S A. 2016 May 17;113(20):5598-603. doi:, 10.1073/pnas.1600486113. Epub 2016 Apr 25. PMID:27114550 doi:http://dx.doi.org/10.1073/pnas.1600486113
- ↑ Desguin B, Fellner M, Riant O, Hu J, Hausinger R, Hols P, Soumillion P. Biosynthesis of the nickel-pincer nucleotide cofactor of lactate racemase requires a CTP-dependent cyclometallase. J Biol Chem. 2018 Jun 10. pii: RA118.003741. doi: 10.1074/jbc.RA118.003741. PMID:29887527 doi:http://dx.doi.org/10.1074/jbc.RA118.003741
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