3abi | pdb_00003abi

Crystal Structure of L-Lysine Dehydrogenase from Hyperthermophilic Archaeon Pyrococcus horikoshii

spinqualitylabelsall models 3abi, resolution 2.44Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3abi is a 2 chain structure with sequence from Pyrococcus horikoshii. This structure supersedes the now removed PDB entries and 2z2v. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: NAD, SO4 Gene: PH1688 (Pyrococcus horikoshii) Activity: Lysine 6-dehydrogenase, with EC number 1.4.1.18 Resources: FirstGlance, OCA, RCSB, PDBsum Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed A gene encoding an L-lysine dehydrogenase was identified in the hyperthermophilic archaeon Pyrococcus horikoshii. The gene was overexpressed in Escherichia coli, and its product was purified and characterized. The expressed enzyme is the most thermostable L-lysine dehydrogenase yet described, with a half-life of 180 min at 100 degrees C. The product of the enzyme's catalytic activity is Delta(1)-piperideine-6-carboxylate, which makes this enzyme an L-lysine 6-dehydrogenase (EC 1.4.1.18) that catalyzes the reductive deamination of the epsilon- amino group and a type of NAD-dependent amine dehydrogenase. The three-dimensional structure of the enzyme was determined using the mercury-based multiple-wavelength anomalous dispersion method at a resolution of 2.44 A in the presence of NAD and sulfate ion. The asymmetric unit consisted of two subunits, and a crystallographic 2-fold axis generated the functional dimer. Each monomer consisted of a Rossmann fold domain and a C-terminal catalytic domain, and the fold of the catalytic domain showed similarity to that of saccharopine reductase. Notably, the structures of subunits A and B differed significantly. In subunit A, the active site contained a sulfate ion that was not seen in subunit B. Consequently, subunit A adopted a closed conformation, whereas subunit B adopted an open one. In each subunit, one NAD molecule was bound to the active site in an anti-conformation, indicating that the enzyme makes use of pro-R-specific hydride transfer between the two hydrides at C-4 of NADH (type A specificity). This is the first description of the three-dimensional structure of l-lysine 6-dehydrogenase as an NAD-dependent amine dehydrogenase. First crystal structure of L-lysine 6-dehydrogenase as an NAD-dependent amine dehydrogenase.,Yoneda K, Fukuda J, Sakuraba H, Ohshima T J Biol Chem. 2010 Mar 12;285(11):8444-53. Epub 2010 Jan 7. PMID:20056607 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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