5j83: Difference between revisions
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The | ==Crystal structure of L-arabinonate dehydratase in apo-form== | ||
<StructureSection load='5j83' size='340' side='right'caption='[[5j83]], [[Resolution|resolution]] 3.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5j83]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhizobium_leguminosarum_bv._trifolii Rhizobium leguminosarum bv. trifolii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J83 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J83 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]] 3.001Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</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=5j83 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j83 OCA], [https://pdbe.org/5j83 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j83 RCSB], [https://www.ebi.ac.uk/pdbsum/5j83 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j83 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/I9XDU6_RHILT I9XDU6_RHILT] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
We present a novel crystal structure of the IlvD/EDD family enzyme, l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT, EC 4.2.1.25), which catalyzes the conversion of l-arabinonate to 2-dehydro-3-deoxy-l-arabinonate. The enzyme is a tetramer consisting of a dimer of dimers, where each monomer is composed of two domains. The active site contains a catalytically important [2Fe-2S] cluster and Mg(2+) ion and is buried between two domains, and also at the dimer interface. The active site Lys129 was found to be carbamylated. Ser480 and Thr482 were shown to be essential residues for catalysis, and the S480A mutant structure showed an unexpected open conformation in which the active site was more accessible for the substrate. This structure showed the partial binding of l-arabinonate, which allowed us to suggest that the alkoxide ion form of the Ser480 side chain functions as a base and the [2Fe-2S] cluster functions as a Lewis acid in the elimination reaction. | |||
The Crystal Structure of a Bacterial l-Arabinonate Dehydratase Contains a [2Fe-2S] Cluster.,Rahman MM, Andberg M, Thangaraj SK, Parkkinen T, Penttila M, Janis J, Koivula A, Rouvinen J, Hakulinen N ACS Chem Biol. 2017 Jul 21;12(7):1919-1927. doi: 10.1021/acschembio.7b00304. Epub, 2017 Jun 13. PMID:28574691<ref>PMID:28574691</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5j83" style="background-color:#fffaf0;"></div> | ||
[[Category: Hakulinen | == References == | ||
[[Category: Rouvinen | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Rhizobium leguminosarum bv. trifolii]] | |||
[[Category: Hakulinen N]] | |||
[[Category: Rahman MM]] | |||
[[Category: Rouvinen J]] | |||
Latest revision as of 10:53, 6 September 2023
Crystal structure of L-arabinonate dehydratase in apo-form
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