5na1 | pdb_00005na1

NADH:quinone oxidoreductase (NDH-II) from Staphylococcus aureus - holoprotein structure - 2.32 A resolution

spinqualitylabelsall models 5na1, resolution 2.32Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5na1 is a 1 chain structure with sequence from Staphylococcus aureus subsp. aureus NCTC 8325. This structure supersedes the now removed PDB entry 4xdb. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.32Å Ligands: FAD, MLI, PO4 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function NDH_STAA8 Alternative, nonproton pumping NADH:quinone oxidoreductase that delivers electrons to the respiratory chain by oxidation of NADH and reduction of quinones, and contributes to the regeneration of NAD(+) (PubMed:26172206, PubMed:28801048). Can use DMN, a menaquinone analog, 2,3-dimethoxy-5,6-dimethyl-benzoquinone (DDB), an ubiquinone analog, or 2,3,5,6-tetramethyl-1,4-benzoquinone (Duroquinone, DQ) a plastoquinone analog as electron acceptors (PubMed:26172206). Publication Abstract from PubMed Type II NADH:quinone oxidoreductases (NDH-2s) are membrane bound enzymes that deliver electrons to the respiratory chain by oxidation of NADH and reduction of quinones. In this way, these enzymes also contribute to the regeneration of NAD(+), allowing several metabolic pathways to proceed. As for the other members of the two-Dinucleotide Binding Domains Flavoprotein (tDBDF) superfamily, the enzymatic mechanism of NDH-2s is still little explored and elusive. In this work we addressed the role of the conserved glutamate 172 (E172) residue in the enzymatic mechanism of NDH-2 from Staphylococcus aureus. We aimed to test our earlier hypothesis that E172 plays a key role in proton transfer to allow the protonation of the quinone. For this we performed a complete biochemical characterization of the enzyme's variants E172A, E172Q and E172S. Our steady state kinetic measurements show a clear decrease in the overall reaction rate, and our substrate interaction studies indicate the binding of the two substrates is also affected by these mutations. Interestingly our fast kinetic results show quinone reduction is more affected than NADH oxidation. We have also determined the X-ray crystal structure of the E172S mutant (2.55A) and compared it with the structure of the wild type (2.32A). Together these results support our hypothesis for E172 being of central importance in the catalytic mechanism of NDH-2, which may be extended to other members of the tDBDF superfamily. The key role of glutamate 172 in the mechanism of type II NADH:quinone oxidoreductase of Staphylococcus aureus.,Sousa FM, Sena FV, Batista AP, Athayde D, Brito JA, Archer M, Oliveira ASF, Soares CM, Catarino T, Pereira MM Biochim Biophys Acta. 2017 Oct;1858(10):823-832. doi:, 10.1016/j.bbabio.2017.08.002. Epub 2017 Aug 8. PMID:28801048 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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