6d6z: Difference between revisions
New page: '''Unreleased structure''' The entry 6d6z is ON HOLD until Apr 23 2020 Authors: Fellner, M., Hausinger, R.P., Hu, J. Description: Structure of the 2nd lactate racemase homolog apoprote... |
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==Structure of the malate racemase apoprotein from Thermoanaerobacterium thermosaccharolyticum== | |||
<StructureSection load='6d6z' size='340' side='right'caption='[[6d6z]], [[Resolution|resolution]] 2.38Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6d6z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoanaerobacterium_thermosaccharolyticum_DSM_571 Thermoanaerobacterium thermosaccharolyticum DSM 571]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D6Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6D6Z FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.38Å</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=6d6z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d6z OCA], [https://pdbe.org/6d6z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d6z RCSB], [https://www.ebi.ac.uk/pdbsum/6d6z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d6z ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/D9TSN9_THETC D9TSN9_THETC] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Isomerization reactions are fundamental in biology. Lactate racemase, which isomerizes L- and D-lactate, is composed of the LarA protein and a nickel-containing cofactor, the nickel-pincer nucleotide (NPN). In this study, we show that LarA is part of a superfamily containing many different enzymes. We overexpressed and purified 13 lactate racemase homologs, incorporated the NPN cofactor, and assayed the isomerization of different substrates guided by gene context analysis. We discovered two malate racemases, one phenyllactate racemase, one alpha-hydroxyglutarate racemase, two D-gluconate 2-epimerases, and one short-chain aliphatic alpha-hydroxyacid racemase among the tested enzymes. We solved the structure of a malate racemase apoprotein and used it, along with the previously described structures of lactate racemase holoprotein and D-gluconate epimerase apoprotein, to identify key residues involved in substrate binding. This study demonstrates that the NPN cofactor is used by a diverse superfamily of alpha-hydroxyacid racemases and epimerases, widely expanding the scope of NPN-dependent enzymes. | |||
Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases.,Desguin B, Urdiain-Arraiza J, Da Costa M, Fellner M, Hu J, Hausinger RP, Desmet T, Hols P, Soumillion P Sci Rep. 2020 Oct 22;10(1):18123. doi: 10.1038/s41598-020-74802-6. PMID:33093595<ref>PMID:33093595</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6d6z" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Thermoanaerobacterium thermosaccharolyticum DSM 571]] | |||
[[Category: Fellner M]] | |||
[[Category: Hausinger RP]] | |||
[[Category: Hu J]] | |||
Latest revision as of 18:19, 4 October 2023
Structure of the malate racemase apoprotein from Thermoanaerobacterium thermosaccharolyticumStructure of the malate racemase apoprotein from Thermoanaerobacterium thermosaccharolyticum
Structural highlights
FunctionPublication Abstract from PubMedIsomerization reactions are fundamental in biology. Lactate racemase, which isomerizes L- and D-lactate, is composed of the LarA protein and a nickel-containing cofactor, the nickel-pincer nucleotide (NPN). In this study, we show that LarA is part of a superfamily containing many different enzymes. We overexpressed and purified 13 lactate racemase homologs, incorporated the NPN cofactor, and assayed the isomerization of different substrates guided by gene context analysis. We discovered two malate racemases, one phenyllactate racemase, one alpha-hydroxyglutarate racemase, two D-gluconate 2-epimerases, and one short-chain aliphatic alpha-hydroxyacid racemase among the tested enzymes. We solved the structure of a malate racemase apoprotein and used it, along with the previously described structures of lactate racemase holoprotein and D-gluconate epimerase apoprotein, to identify key residues involved in substrate binding. This study demonstrates that the NPN cofactor is used by a diverse superfamily of alpha-hydroxyacid racemases and epimerases, widely expanding the scope of NPN-dependent enzymes. Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases.,Desguin B, Urdiain-Arraiza J, Da Costa M, Fellner M, Hu J, Hausinger RP, Desmet T, Hols P, Soumillion P Sci Rep. 2020 Oct 22;10(1):18123. doi: 10.1038/s41598-020-74802-6. PMID:33093595[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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