5j83 | pdb_00005j83

Crystal structure of L-arabinonate dehydratase in apo-form

spinqualitylabelsall models 5j83, resolution 3.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5j83 is a 2 chain structure with sequence from Rhizobium leguminosarum bv. trifolii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 3.001Å Ligands: KCX Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function I9XDU6_RHILT 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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