6rtu

Piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus complexed with alpha-aminoadipic acid

spinqualitylabelsall models 6rtu, resolution 1.90Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6rtu is a 2 chain structure with sequence from Streptomyces clavuligerus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.9Å Ligands: ACT, GOL, SO4, UN1 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function O85725_STRCL Publication Abstract from PubMed The core of beta-lactam antibiotics originates from amino acids of primary metabolism in certain microorganisms. beta-Lactam-producing bacteria, including Streptomyces clavuligerus, synthesize the precursor of the amino acid alpha-aminoadipic acid by the catabolism of lysine in two steps. The second reaction, the oxidation of piperideine-6-carboxylate (or its open-chain form alpha-aminoadipate semialdehyde) to alpha-aminoadipic acid, is catalysed by the NAD(+)-dependent enzyme piperideine-6-carboxylate dehydrogenase (P6CDH). This structural study, focused on ligand binding and catalysis, presents structures of P6CDH from S. clavuligerus in its apo form and in complexes with the cofactor NAD(+), the product alpha-aminoadipic acid and a substrate analogue, picolinic acid. P6CDH adopts the common aldehyde dehydrogenase fold, consisting of NAD-binding, catalytic and oligomerization domains. The product binds in the oxyanion hole, close to the catalytic residue Cys299. Clear density is observed for the entire cofactor, including the nicotinamide riboside, in the binary complex. NAD(+) binds in an extended conformation with its nicotinamide ring overlapping with the binding site of the carboxylate group of the product, implying that the conformation of the cofactor may change during catalysis. The binding site of the substrate analogue overlaps with that of the product, suggesting that the cyclic form of the substrate, piperideine-6-carboxylate, may be accepted as a substrate by the enzyme. The catalytic mechanism and the roles of individual residues are discussed in light of these results. Structure and mechanism of piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus.,Hasse D, Hulsemann J, Carlsson GH, Valegard K, Andersson I Acta Crystallogr D Struct Biol. 2019 Dec 1;75(Pt 12):1107-1118. doi:, 10.1107/S2059798319014852. Epub 2019 Nov 22. PMID:31793904 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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