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6utt

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

Structural highlights

6utt is a 6 chain structure with sequence from Lactiplantibacillus plantarum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.49Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2]

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^[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
↑ Fellner M, Huizenga KG, Hausinger RP, Hu J. Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE. Sci Rep. 2020 Apr 2;10(1):5830. doi: 10.1038/s41598-020-62847-6. PMID:32242052 doi:http://dx.doi.org/10.1038/s41598-020-62847-6

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6utt"

@@ Line 3: / Line 3: @@
 <StructureSection load='6utt' size='340' side='right'caption='[[6utt]], [[Resolution|resolution]] 2.49&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6utt]] 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=6UTT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6UTT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6utt]] 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=6UTT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UTT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.49&#8491;</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=CA:CALCIUM+ION'>CA</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=6utt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6utt OCA], [http://pdbe.org/6utt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6utt RCSB], [http://www.ebi.ac.uk/pdbsum/6utt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6utt 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=6utt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6utt OCA], [https://pdbe.org/6utt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6utt RCSB], [https://www.ebi.ac.uk/pdbsum/6utt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6utt ProSAT]</span></td></tr>
 </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;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Lactobacillus arabinosus fred et al]]
+[[Category: Lactiplantibacillus plantarum]]
 [[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: Lare]]
-[[Category: Pp-loop]]
-[[Category: Sulfur transferase]]
-[[Category: Transferase]]

6utt

From Proteopedia

Current revision

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

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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