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Figure 6
Details of the catalytic mechanism of bacterial (Class 1) type 2 asparaginases. The panels show structures of the K162M mutant of EcAII, in which (5)Lys was replaced by (5)Met*. (a) Acyl-enzyme intermediate (PDB entry 6v2g). (b) Tetrahedral intermediate TI2 (PDB entry 6v25). Residues and waters (W1, W2, W3) participating in proton shuttling from (1)Thr to (4)Asp via (2)Tyr are colored cyan. (3)Thr and (5)Met* (corresponding to (5)Lys in the wild-type protein) are colored green. Red dashed lines represent hydrogen bonds between waters and residues involved in catalysis. Magenta dotted lines show the interactions stabilizing the TI2 intermediate in the oxyanion hole formed by the carbonyl O atom of (8)Ala and the conserved water molecule W1. A fat pink arrow marks the position of water W2 in (a), which is incorporated into TI2 in (b). Black dashed lines represent hydrogen bonds anchoring the substrate/product in the active site. Some less important hydrogen bonds were omitted for clarity. A brown curved arrow indicates the direction of the nucleophilic attack of water W2 on the acyl-enzyme intermediate.

IUCrJ
Volume 8| Part 4| July 2021| Pages 514-531
ISSN: 2052-2525
https://doi.org/10.1107/S2052252521006011