Structural and biophysical aspects of l-asparaginases: a growing family with amazing diversity

Loch, J.I.; Jaskolski, M.

doi:10.1107/S2052252521006011

Figure 5
(a)–(e) Steps in the catalytic mechanism of type 2 bacterial (Class 1) L-asparaginases based on the reactions proposed by Lubkowski et al. (2020

). Residues and waters (3×) involved in proton shuttling from ⁽¹⁾Thr to ⁽⁴⁾Asp via ⁽²⁾Tyr are colored blue. ⁽³⁾Thr and ⁽⁵⁾Lys that exchange protons with conserved water W2 (red) are colored green. ⁽⁴⁾Ala (carbonyl O atom) and W1 creating the oxyanion hole are colored magenta (the carbonyl O atom of ⁽¹⁾Thr, which is also part of the oxyanion hole, is not shown). ⁽⁶⁾Ser participating in substrate/product anchoring, the L-Asn substrate, intermediate products and the L-Asp end product are colored black (substrate/product is also hydrogen-bonded to ⁽⁷⁾Gln, ⁽⁸⁾Ala, ⁽⁹⁾Asn′ and ⁽¹⁰⁾Glu′, but these interactions are not shown in the figure). (f)–(j) Steps of the catalytic mechanism of Class 2 L-asparaginases based on the reactions proposed by Nomme et al. (2012

). Protein residues involved in catalysis are colored blue, residues creating the oxyanion hole are colored magenta and water molecules important for catalysis are colored red, ⁽¹⁰⁴⁾Arg important for substrate anchoring is colored black (substrate/product is also hydrogen-bonded to ⁽¹⁰³⁾Thr, ⁽¹⁰⁶⁾Gly, ⁽¹⁰⁵⁾Asp and ⁽¹⁰⁷⁾Gly, but these interactions are not shown in the figure). In all panels, the directions of the nucleophilic attacks are shown by brown arrows. For clarity, only the functional groups of the protein residues are shown in atomic detail; the remainder is marked by a circle. In all panels, the substrate/product molecules are colored black and shaded.

IUCrJ

Volume 8| Part 4| July 2021| Pages 514-531

ISSN: 2052-2525

https://doi.org/10.1107/S2052252521006011

BIOLOGY | MEDICINE

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