Journal:Acta Cryst F:S2053230X24003911
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The catalytic subunit from Desulfovibrio vulgaris FdhAB contains a W center, coordinating two Molybdopterin Guanine Dinucleotides (MGD), one terminal sulfido ligand (-SH/=S) and a SeCys (selenocysteine) residue from the polypeptide chain, in a distorted trigonal prismatic geometry. In the second coordination sphere of the metal, two conserved residues are catalytically relevant: a histidine, thought to play a role in proton transfer, and an arginine involved in substrate orientation and stabilization of putative catalytic intermediates <ref name="a1">doi: 10.1021/acscatal.0c00086</ref>. | The catalytic subunit from Desulfovibrio vulgaris FdhAB contains a W center, coordinating two Molybdopterin Guanine Dinucleotides (MGD), one terminal sulfido ligand (-SH/=S) and a SeCys (selenocysteine) residue from the polypeptide chain, in a distorted trigonal prismatic geometry. In the second coordination sphere of the metal, two conserved residues are catalytically relevant: a histidine, thought to play a role in proton transfer, and an arginine involved in substrate orientation and stabilization of putative catalytic intermediates <ref name="a1">doi: 10.1021/acscatal.0c00086</ref>. | ||
A recently discovered disulphide redox switch was shown to be crucial in an allosteric mechanism for enzyme activation (yielding maximum activity) or inactivation (resulting in protection against O2 damage) <ref name="a2">pmid 37985883</ref>. This allosteric mechanism makes use of conformational changes that extend from the surface exposed disulfide bond towards the deeply buried residue M405 near the active site, adopting new conformations. | A recently discovered disulphide redox switch was shown to be crucial in an allosteric mechanism for enzyme activation (yielding maximum activity) or inactivation (resulting in protection against O2 damage) <ref name="a2">pmid 37985883</ref>. This allosteric mechanism makes use of conformational changes that extend from the surface exposed disulfide bond towards the deeply buried residue M405 near the active site, adopting new conformations. | ||
| - | 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/2'>Wildtype</scene> and <scene name='10/1045788/M405s/4'>W-DvFdhAB M405S</scene> active sites. <scene name='10/1045788/Superposition/ | + | 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/2'>Wildtype</scene> and <scene name='10/1045788/M405s/4'>W-DvFdhAB M405S</scene> active sites. <scene name='10/1045788/Superposition/7'>A superposition of the M405S variant (black) and the oxidized WT</scene> (red; PDB entry [[6sdr]]), only selected atoms of MGD1 are show for clarity. 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/4'>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/4'>The M405S variant</scene> (PDB entry [[8rcg]]). | *<scene name='10/1045788/M405sbf/4'>The M405S variant</scene> (PDB entry [[8rcg]]). | ||
*<scene name='10/1045788/M405a/4'>The M405A variant</scene> (PDB entry [[8cm7]]). The loop Gly896–Ile992, was not modelled for this data set. | *<scene name='10/1045788/M405a/4'>The M405A variant</scene> (PDB entry [[8cm7]]). The loop Gly896–Ile992, was not modelled for this data set. | ||
Revision as of 14:00, 13 May 2024
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