Structural analysis of YcdY, a member of the redox-enzyme maturation protein family

Choi, H.J.; Lee, S.; Kim, J.-H.; You, Y.-B.; Yoon, S.

doi:10.1107/S2053230X25003887

Figure 3
Structural analysis of the enYcdY dent. (a) The relatively neutral property of the enYcdY dent in the electrostatic potential surface of the enYcdY structure (positive, blue; neutral, white; negative, red). The electrostatic potential was calculated using the APBS module implemented in PyMOL (https://pymol.org/). The enYcdY dent is indicated by a yellow dashed ellipse. (b) High sequence conservation of the enYcdY dent. Sequence conservation calculated by the ConSurf server (https://consurf.tau.ac.il/) is proportional to the magenta intensity in the enYcdY structure (surfaces). The enYcdY dent is indicated by a yellow dashed ellipse. (c) enYcdY dent residues. On the enYcdY structure (gray ribbons), the enYcdY residues in the dent are indicated by sticks of different colors on the basis of residue polarity and conservation (yellow, apolar; orange, polar and highly conserved). (d) Structure of enYcdY (surfaces) with the esNarG signal peptide (cyan coils) from the esNarJ–esNarG complex structure (PDB entry 8jzd) overlaid on the enYcdY structure. The enYcdY structure is shown as sequence conservation-coded surfaces, as depicted in Fig. 3

(b). The enYcdY dent is indicated by a yellow dashed ellipse.

STRUCTURAL BIOLOGY
COMMUNICATIONS

ISSN: 2053-230X

Volume 81| Part 6| June 2025| Pages 263-271

https://doi.org/10.1107/S2053230X25003887

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