5udx

From Proteopedia

(Difference between revisions)

Current revision

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

Structural highlights

5udx is a 6 chain structure with sequence from Lactiplantibacillus plantarum WCFS1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.784Å
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

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.

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^[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, Desguin B, Hausinger RP, Hu J. Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE. 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 doi:http://dx.doi.org/10.1073/pnas.1704967114

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/5udx"

@@ Line 1: / Line 1: @@
 ==LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with zinc==
-<StructureSection load='5udx' size='340' side='right' caption='[[5udx]], [[Resolution|resolution]] 2.78&Aring;' scene=''>
+<StructureSection load='5udx' size='340' side='right'caption='[[5udx]], [[Resolution|resolution]] 2.78&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5udx]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UDX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UDX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5udx]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactiplantibacillus_plantarum_WCFS1 Lactiplantibacillus plantarum WCFS1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UDX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.784&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5udq|5udq]], [[5udr|5udr]], [[5uds|5uds]], [[5udt|5udt]], [[5udu|5udu]], [[5udv|5udv]], [[5udw|5udw]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5udx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5udx OCA], [http://pdbe.org/5udx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5udx RCSB], [http://www.ebi.ac.uk/pdbsum/5udx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5udx 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=5udx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5udx OCA], [https://pdbe.org/5udx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5udx RCSB], [https://www.ebi.ac.uk/pdbsum/5udx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5udx 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: Desguin, B]]
+[[Category: Lactiplantibacillus plantarum WCFS1]]
-[[Category: Fellner, M]]
+[[Category: Large Structures]]
-[[Category: Hausinger, R P]]
+[[Category: Desguin B]]
-[[Category: Hu, J]]
+[[Category: Fellner M]]
-[[Category: Ampylation]]
+[[Category: Hausinger RP]]
-[[Category: Atp pyrophophatase domain]]
+[[Category: Hu J]]
-[[Category: Hexamer]]
-[[Category: Lactate]]
-[[Category: Lactate racemase]]
-[[Category: Lactate racemization]]
-[[Category: Lar]]
-[[Category: Lare]]
-[[Category: Pp-loop]]
-[[Category: Sulfur transferase]]
-[[Category: Transferase]]
-[[Category: Trimer]]

5udx

From Proteopedia

Current revision

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

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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