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5huq

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Revision as of 10:54, 16 August 2023

A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase

Structural highlights

5huq is a 2 chain structure with sequence from Lactiplantibacillus plantarum. This structure supersedes the now removed PDB entry 4yns. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LARA_LACPL Catalyzes the interconversion between the D- and L-isomers of lactate (PubMed:24710389, PubMed:26138974). May act as a rescue enzyme to ensure D-lactate production in physiological conditions where its production by the D-lactate dehydrogenase LdhD is not sufficient (PubMed:16166538). D-Lactate is absolutely required for growth of L.plantarum and is an essential component of the cell wall peptidoglycan in this species, where it is incorporated as the last residue of the muramoyl-pentadepsipeptide peptidoglycan precursor; its incorporation confers high level of vancomycin resistance (PubMed:16166538).^[1] ^[2] ^[3]

Publication Abstract from PubMed

Lactic acid racemization is involved in lactate metabolism and cell wall assembly of many microorganisms. Lactate racemase (Lar) requires nickel, but the nickel-binding site and the role of three accessory proteins required for its activation remain enigmatic. We combined mass spectrometry and x-ray crystallography to show that Lar from Lactobacillus plantarum possesses an organometallic nickel-containing prosthetic group. A nicotinic acid mononucleotide derivative is tethered to Lys(184) and forms a tridentate pincer complex that coordinates nickel through one metal-carbon and two metal-sulfur bonds, with His(200) as another ligand. Although similar complexes have been previously synthesized, there was no prior evidence for the existence of pincer cofactors in enzymes. The wide distribution of the accessory proteins without Lar suggests that it may play a role in other enzymes.

METALLOPROTEINS. A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase.,Desguin B, Zhang T, Soumillion P, Hols P, Hu J, Hausinger RP Science. 2015 Jul 3;349(6243):66-9. doi: 10.1126/science.aab2272. PMID:26138974^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Goffin P, Deghorain M, Mainardi JL, Tytgat I, Champomier-Verges MC, Kleerebezem M, Hols P. Lactate racemization as a rescue pathway for supplying D-lactate to the cell wall biosynthesis machinery in Lactobacillus plantarum. J Bacteriol. 2005 Oct;187(19):6750-61. doi: 10.1128/JB.187.19.6750-6761.2005. PMID:16166538 doi:http://dx.doi.org/10.1128/JB.187.19.6750-6761.2005
↑ 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, Zhang T, Soumillion P, Hols P, Hu J, Hausinger RP. METALLOPROTEINS. A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase. Science. 2015 Jul 3;349(6243):66-9. doi: 10.1126/science.aab2272. PMID:26138974 doi:http://dx.doi.org/10.1126/science.aab2272
↑ Desguin B, Zhang T, Soumillion P, Hols P, Hu J, Hausinger RP. METALLOPROTEINS. A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase. Science. 2015 Jul 3;349(6243):66-9. doi: 10.1126/science.aab2272. PMID:26138974 doi:http://dx.doi.org/10.1126/science.aab2272

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/5huq"

@@ Line 3: / Line 3: @@
 <StructureSection load='5huq' size='340' side='right'caption='[[5huq]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5huq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"lactobacillus_arabinosus"_fred_et_al. "lactobacillus arabinosus" fred et al.]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4yns 4yns]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HUQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5HUQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5huq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactiplantibacillus_plantarum Lactiplantibacillus plantarum]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4yns 4yns]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HUQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HUQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4EY:1-[(2R,3R,4S,5R)-3,4-BIS(OXIDANYL)-5-(PHOSPHONOOXYMETHYL)OXOLAN-2-YL]-5-METHANETHIOYL-PYRIDINE-3-CARBOTHIOIC+S-ACID'>4EY</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AB662_09960, ADS73_14595, AKJ11_11795, AN634_09100, AOZ08_01600, IV39_GL000121, JM48_0086, Nizo2877_0389, WU67_00115 ([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=4EY:1-[(2R,3R,4S,5R)-3,4-BIS(OXIDANYL)-5-(PHOSPHONOOXYMETHYL)OXOLAN-2-YL]-5-METHANETHIOYL-PYRIDINE-3-CARBOTHIOIC+S-ACID'>4EY</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=5huq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5huq OCA], [http://pdbe.org/5huq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5huq RCSB], [http://www.ebi.ac.uk/pdbsum/5huq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5huq 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=5huq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5huq OCA], [https://pdbe.org/5huq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5huq RCSB], [https://www.ebi.ac.uk/pdbsum/5huq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5huq ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/LARA_LACPL LARA_LACPL] Catalyzes the interconversion between the D- and L-isomers of lactate (PubMed:24710389, PubMed:26138974). May act as a rescue enzyme to ensure D-lactate production in physiological conditions where its production by the D-lactate dehydrogenase LdhD is not sufficient (PubMed:16166538). D-Lactate is absolutely required for growth of L.plantarum and is an essential component of the cell wall peptidoglycan in this species, where it is incorporated as the last residue of the muramoyl-pentadepsipeptide peptidoglycan precursor; its incorporation confers high level of vancomycin resistance (PubMed:16166538).<ref>PMID:16166538</ref> <ref>PMID:24710389</ref> <ref>PMID:26138974</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: Desguin, B]]
+[[Category: Desguin B]]
-[[Category: Hausinger, R P]]
+[[Category: Hausinger RP]]
-[[Category: Hols, P]]
+[[Category: Hols P]]
-[[Category: Hu, J]]
+[[Category: Hu J]]
-[[Category: Soumillion, P]]
+[[Category: Soumillion P]]
-[[Category: Zhang, T]]
+[[Category: Zhang T]]
-[[Category: Cofactor]]
-[[Category: Isomerase]]
-[[Category: Nickel]]
-[[Category: Racemase]]

5huq

From Proteopedia

Revision as of 10:54, 16 August 2023

A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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