It started off as a Cys, how did it end up like this? Identifying the extent of unmodelled oxidatively modified cysteines within the Protein Data Bank

Foster, S.P.; Warren, A.J.; Siebert, C.A.; Basran, J.; Moody, P.C.E.

doi:10.1107/S2059798326003943

Acta Crystallographica Section D
Acta Crystallographica
Section D STRUCTURAL BIOLOGY

IUCr IT WDC

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Figure 1
Structural basis of hpGAPDHA being nominally reduced. The best fit to the 2mF_o − DF_c (grey, contoured to 1.5σ) and anomalous difference (magenta, contoured to 5.0σ) maps is for a cysteine sulfinic acid (a) (cysteine sulfinic acid shown in the inset) and not the reduced sulfhydryl (b) (initially fitted cysteine in the inset). Crystals soaked in iodoacetamide dissolved; however, crystals produced with iodoacetamide-labelled hpGAPDHA show clear labelling of the active site (c) (carbamidomethylated cysteine presented in purple) and distal cysteines (not shown). As the S_N2 reaction of cysteine with iodoacetamide requires cysteine to be reduced (d), successful labelling with iodoacetamide indicates that Cys149 is oxidized upon X-ray exposure. The PDB code for the NADP holoenzyme structure used in (a) and (b) is 9fq4; the iodoacetamide structure (Foster, 2025