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Fig. 1 | Biology Direct

Fig. 1

From: Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site

Fig. 1

The GPAA1 model with one zinc ion and the substrate analogue. In this illustration, we show the 3D structural model of the lumenal domain of human GPAA1 resulting from the homology modelling effort together with (a) a scheme of the GPI lipid anchor at the endoplasmic reticulum (lipid part is omitted) as its terminal phospho-ethanolamine group reaches into the catalytic cleft where it comes into contact with zinc ion and the ω-site (the C-terminus) of the substrate protein pre-processed by PIG-K. The colour code (red/blue) of the model indicates the time-dependent position of the secondary structural elements along a molecular dynamics trajectory. Visibly, the α / β hydrolase fold, consisting of 8 strands and 7 helices, was maintained during the simulation. In section (b) of the figure, we highlight the five residues equivalent to the canonical Zn-binding sites typical for M28-type enzymes for the cases of one and/or two Zn ions. Dashed lines at the GPAA1 model N- and C-termini indicate that the lumenal domain is only a part of GPAA1 structure with additional loops in the endoplasmic reticulum lumen or cytoplasm and transmembrane regions residing in the endoplasmic reticulum membrane

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