Journal:Acta Cryst F:S2053230X24003911
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In a previous work<ref name="a2">pmid 37985883</ref>, the M405A mutation virtually abolished the catalytic activity, and its structure revealed a significantly distortion of the active site, particularly the protein backbone near SeCys192 (U192), preventing the modeling of U192 side chain and the understanding of its possible catalytic role. Comparison between <scene name='10/1045788/Wt/1'>Wildtype</scene> and <scene name='10/1045788/M405s/3'>W-DvFdhAB M405S</scene> active sites. In this work, the M405S mutation was used to probe the prominent role of M405 on the metal site geometry, as we were able to fully model the W site geometry of this variant. <scene name='10/1045788/M405smutation/3'>The hydrogen bonding between the mutated serine (S405 in the mutant) and the two phosphate groups from MGD1</scene> stabilized the M405S mutant when compared to M405A. The side chain of Ser405 is shown, the Ser405 O<sup>γ</sup>–W distance and the hydrogen bonds established to O2α and O2β from the phosphate groups of MGD1 are shown as dashed lines. Thus, we could confirm, in M405S, the significant rearrangement and increased mobility of the I191-T196 helical region (that contains the mechanistically relevant residues U192 and H193), caused by the absence of the bulky M405 side chain, as well as its impact on the flexibility and geometry of the active site. Effect of the absence of the Met405 side chain on the ''B'' factors of the Cα atoms of Ile191–Thr196 of DvFdhAB: | In a previous work<ref name="a2">pmid 37985883</ref>, the M405A mutation virtually abolished the catalytic activity, and its structure revealed a significantly distortion of the active site, particularly the protein backbone near SeCys192 (U192), preventing the modeling of U192 side chain and the understanding of its possible catalytic role. Comparison between <scene name='10/1045788/Wt/1'>Wildtype</scene> and <scene name='10/1045788/M405s/3'>W-DvFdhAB M405S</scene> active sites. In this work, the M405S mutation was used to probe the prominent role of M405 on the metal site geometry, as we were able to fully model the W site geometry of this variant. <scene name='10/1045788/M405smutation/3'>The hydrogen bonding between the mutated serine (S405 in the mutant) and the two phosphate groups from MGD1</scene> stabilized the M405S mutant when compared to M405A. The side chain of Ser405 is shown, the Ser405 O<sup>γ</sup>–W distance and the hydrogen bonds established to O2α and O2β from the phosphate groups of MGD1 are shown as dashed lines. Thus, we could confirm, in M405S, the significant rearrangement and increased mobility of the I191-T196 helical region (that contains the mechanistically relevant residues U192 and H193), caused by the absence of the bulky M405 side chain, as well as its impact on the flexibility and geometry of the active site. Effect of the absence of the Met405 side chain on the ''B'' factors of the Cα atoms of Ile191–Thr196 of DvFdhAB: | ||
*<scene name='10/1045788/M405sbf/3'>The M405S variant</scene>. | *<scene name='10/1045788/M405sbf/3'>The M405S variant</scene>. | ||
| + | *<scene name='10/1045788/M405a/3'>The M405A variant</scene> (PDB entry [[8cm7]]). The loop Gly896–Ile992, was not modelled for this data set. | ||
In all scenes, the tungsten active site and the proximal [4Fe–4S] cluster are shown as sticks and spheres, the peptide chain is shown in ribbon representation. ''B'' factors were normalized for each structure independently. <scene name='10/1045788/Test/7'>Test</scene>. | In all scenes, the tungsten active site and the proximal [4Fe–4S] cluster are shown as sticks and spheres, the peptide chain is shown in ribbon representation. ''B'' factors were normalized for each structure independently. <scene name='10/1045788/Test/7'>Test</scene>. | ||
Revision as of 13:36, 12 May 2024
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