9eid: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 9eid is ~~ON HOLD~~

==A broad-substrate spectrum lactate racemase A from Isosphaera pallida in complex with D-2-Hydroxybutyrate==

== Structural highlights ==

<table><tr><td colspan='2'>[[9eid]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Isosphaera_pallida Isosphaera pallida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9EID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9EID 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]] 1.38Å</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=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UCU:(2~{R})-2-oxidanylbutanoic+acid'>UCU</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=9eid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9eid OCA], [https://pdbe.org/9eid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9eid RCSB], [https://www.ebi.ac.uk/pdbsum/9eid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9eid ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/E8QWZ4_ISOPI E8QWZ4_ISOPI]

== Publication Abstract from PubMed ==

The LarA family consists of diverse racemases/epimerases that interconvert the diastereomers of a variety of alpha-hydroxyacids by using a nickel-pincer nucleotide (NPN) cofactor. The hidden redox reaction catalyzed by the NPN cofactor makes LarA enzymes attractive engineering targets for applications. However, how a LarA enzyme binds its natural substrate and recognizes different alpha-hydroxyacids has not been elucidated. Here, we report three high-resolution structures of the enzyme-substrate complexes of a broad-spectrum LarA enzyme from Isosphaera pallida (LarA (Ip) ). The substrate binding mode reveals an optimal orientation and distance between the hydride donor and acceptor, strongly supporting the proposed proton-coupled hydride transfer mechanism. The experimentally solved structures, together with the structural models of other LarA enzymes, allow us to identify the residues/structural elements critically involved in the interactions with different alpha-hydroxyacid substrates. Collectively, this work provides a critical structural basis for catalysis and substrate recognition of the diverse enzymes in the LarA family, thus building a foundation for enzyme engineering.

~~Authors~~:

Structural Basis for Catalysis and Substrate Specificity of a LarA Racemase with a Broad Substrate Spectrum.,Gatreddi S, Urdiain-Arraiza J, Desguin B, Hausinger RP, Hu J bioRxiv [Preprint]. 2024 Nov 28:2024.11.28.625916. doi: , 10.1101/2024.11.28.625916. PMID:39651260<ref>PMID:39651260</ref>

~~Description~~:

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

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Isosphaera pallida]]

[[Category: Large Structures]]

[[Category: Gatreddi S]]

[[Category: Hausinger RP]]

[[Category: Hu J]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9eid is ON HOLD
+==A broad-substrate spectrum lactate racemase A from Isosphaera pallida in complex with D-2-Hydroxybutyrate==
+<StructureSection load='9eid' size='340' side='right'caption='[[9eid]], [[Resolution|resolution]] 1.38&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9eid]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Isosphaera_pallida Isosphaera pallida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9EID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9EID 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]] 1.38&#8491;</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=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UCU:(2~{R})-2-oxidanylbutanoic+acid'>UCU</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=9eid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9eid OCA], [https://pdbe.org/9eid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9eid RCSB], [https://www.ebi.ac.uk/pdbsum/9eid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9eid ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/E8QWZ4_ISOPI E8QWZ4_ISOPI]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The LarA family consists of diverse racemases/epimerases that interconvert the diastereomers of a variety of alpha-hydroxyacids by using a nickel-pincer nucleotide (NPN) cofactor. The hidden redox reaction catalyzed by the NPN cofactor makes LarA enzymes attractive engineering targets for applications. However, how a LarA enzyme binds its natural substrate and recognizes different alpha-hydroxyacids has not been elucidated. Here, we report three high-resolution structures of the enzyme-substrate complexes of a broad-spectrum LarA enzyme from Isosphaera pallida (LarA (Ip) ). The substrate binding mode reveals an optimal orientation and distance between the hydride donor and acceptor, strongly supporting the proposed proton-coupled hydride transfer mechanism. The experimentally solved structures, together with the structural models of other LarA enzymes, allow us to identify the residues/structural elements critically involved in the interactions with different alpha-hydroxyacid substrates. Collectively, this work provides a critical structural basis for catalysis and substrate recognition of the diverse enzymes in the LarA family, thus building a foundation for enzyme engineering.
-Authors:
+Structural Basis for Catalysis and Substrate Specificity of a LarA Racemase with a Broad Substrate Spectrum.,Gatreddi S, Urdiain-Arraiza J, Desguin B, Hausinger RP, Hu J bioRxiv [Preprint]. 2024 Nov 28:2024.11.28.625916. doi: , 10.1101/2024.11.28.625916. PMID:39651260<ref>PMID:39651260</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 9eid" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Isosphaera pallida]]
+[[Category: Large Structures]]
+[[Category: Gatreddi S]]
+[[Category: Hausinger RP]]
+[[Category: Hu J]]