Sandbox Reserved 1094

This Sandbox is Reserved from 25/11/2019, through 30/9/2020 for use in the course "Structural Biology" taught by Bruno Kieffer at the University of Strasbourg, ESBS. This reservation includes Sandbox Reserved 1091 through Sandbox Reserved 1115.

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Glucose-6-Phosphate Dehydrogenase from Leuconostoc mesenteroides

spinqualitylabelsall models Caption for this structure Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D The protein Glucose-6-Phosphate Dehydrogenase is an enzyme involved in the metabolic pathways of the majority of organisms. Leuconostoc mesenteroides is a Bacilli Gram-positive bacterium that expresses this enzyme. Function G6PD plays an important role in the metabolism of L.mesenteroides. L.mesenteroides is a facultactively anaerobic micro-organism which metabolizes glucose to generate lactic acid, ethanol but also carbon dioxyde. This glucose metabolic process (glycolysis and pentose phosphate pathway) is catalysed by G6PD. During this process, NADH is synthesised and used in the heterolactic fermentation and the biosynthesis of fatty acids. The protein G6PD also has a role in protecting cells from destruction as it produces the co-factor NADPH which plays a role in protecting cells from reactive oxygen species . Genomic context It is coded by the G6PD gene (1461 nucleotides). It has in total 2 chains. In the link below, these two chains are represented by one unique sequence entity. External resource : click on [1] to see the graphical representation on the RCSB website. Catalytic activity D-glucose 6-phosphate + NAD+ → 6-phospho-D-glucono-1,5-lactone + H+ + NADH KM=114 µM for G6PD (with NADP), KM=69 µM for G6PD (with NAD), KM=8.0 µM for NADP, KM=160 µM for NAD. Its regulation depends on the concentration of substrate and coenzyme, rate limiting step in pentose phosphate pathway. Optimum pH for its activity is 5.4 - 8.9. Evolutionary conservation The different structures conserved evolutionary can be observed according to the scale following. Check, as determined by ConSurfDB. Mutations Mutagenesis of this enzyme induces catalytic activity loss: more than 200 mutations have been identified. A mutation in a nucleotide in the sequence coding for G6PD leads to disruption of the normal expression of the enzyme, or to a disruption in the amino acid structure of the enzyme which leads to a loss or decrease of catalytic activity toward its substrate. The most common mutations in the amino acids sequence found that induce a loss of catalytic activity are a substitution of the bold amino acids by another one: MVSEIKTLVT FFGG T GDLAK R TK LYPSVFNL YKKGYLQKHF AIVGTA RQ AL NDDEFKQLVR DSIKDFTDDQ AQAEAFIEHF SYRAHDVTDA ASYAVLKEAI EEAADKFDID GNRIFYMSVA PRFFGTIAKY LKSEGLLADT GYNRLMIEK P FGTSYDTAAE LQNDLENAFD DNQLFRI DHY LG K EMVQNIA ALRFGNPIFD AAWNKDYIKN VQVTLSEVLG VEERAGYYDT AGALLDMIQN H TMQIVGWLA MEKPESFTDK DIRAAKNAAF NALKIYDEAE VNKYFVRAQY GAGDSADFKP YLEELDVPAD SKNNTFIAGE LQFDLPRWEG VPFYVRSGKR LAA K QTRVDI VFKAGTFNFG SEQEAQEAVL SIII D PKGAI ELKLNAKSVE DAFNTRTIDL GWTVSDEDKK NTPEP Y ERMI HDTMNGDGSN FADWNGVSIA WKFVDAISAV YTADKAPLET YKSGSMGPEA SDKLLAANGD AWVFKG. This sequence being the normal protein sequence found in L. mesenteroides. Structural highlights Glucose-6-Phosphate Dehydrogenase is formed of a homodimer, so a dimer of two identical subunit. Secondary structure A subunit contains 485 residues where 285 residues are in secondary structure. 93 residues are involved in 15 β-sheet strands and 192 in 17 helices. Tertiary structure Each monomer is composed of 2 domains, 1 red and 1 green. Depending on several conditions, it can dimerize to form tetramers. Each monomer is composed of a small domain localized in the amino terminal part which constitute the coenzyme binding domain and a larger domain in the carboxy terminal part which constitute the substrate binding domain. the complex has a substrate binding site that binds to G6P, and a catalytic coenzyme binding site that binds to NADP+ using the Rossman fold. Coenzyme binding domain The coenzyme binding domain binds the NAD or NADP which participes in the dehydrogenation of G6P. It is defined by a typical β-α-β dinucleotide-binding fold corresponding to a Rossman fold. Substrate binding domain The substrate binding domain binds to the 6-phosphate of G6P. It is defined by a β+α particular fold which has created his own fold family the G6PD-like. It is composed of a large essentially antiparallel curved nine-stranded β-sheet with 11 helices. Quaternary structure Dimer The dimer is very extend compared to the monomer with a size of 112Å. The enzyme is found into a dimeric form in vivo. The two subunits interface is made by the contact between the two antiparallels β-sheets of the substrate binding domains. Their interaction is crucial and form a β-half-barrel on one side of the protein which is closed on the other side by helices of each monomer. The majority of dimer contacts are hydrophobic but there are three salt bridges, especially a conserved one between Glu183 and Lys386, and two main chain hydrogen bonds which participates to the cohesion of the structure. The active site of the enzyme is contained in each monomer but the dimeric form is necessary to the biological activity indeed it confers the stability in aqueous medium.

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