6V28
Complex of double mutant (T89V,K162T) of E. coli L-asparaginase II with L-Asp
Summary for 6V28
| Entry DOI | 10.2210/pdb6v28/pdb |
| Descriptor | L-asparaginase 2, IMIDAZOLE, GLYCEROL, ... (4 entities in total) |
| Functional Keywords | l-asparagine hydrolase, anti-cancer drug, inactive mutant, hydrolase |
| Biological source | Escherichia coli (strain K12) |
| Total number of polymer chains | 4 |
| Total formula weight | 143470.48 |
| Authors | Lubkowski, J.,Wlodawer, A. (deposition date: 2019-11-22, release date: 2020-05-20, Last modification date: 2023-10-11) |
| Primary citation | Lubkowski, J.,Vanegas, J.,Chan, W.K.,Lorenzi, P.L.,Weinstein, J.N.,Sukharev, S.,Fushman, D.,Rempe, S.,Anishkin, A.,Wlodawer, A. Mechanism of Catalysis by l-Asparaginase. Biochemistry, 59:1927-1945, 2020 Cited by PubMed Abstract: Two bacterial type II l-asparaginases, from and , have played a critical role for more than 40 years as therapeutic agents against juvenile leukemias and lymphomas. Despite a long history of successful pharmacological applications and the apparent simplicity of the catalytic reaction, controversies still exist regarding major steps of the mechanism. In this report, we provide a detailed description of the reaction catalyzed by type II l-asparaginase (EcAII). Our model was developed on the basis of new structural and biochemical experiments combined with previously published data. The proposed mechanism is supported by quantum chemistry calculations based on density functional theory. We provide strong evidence that EcAII catalyzes the reaction according to the double-displacement (ping-pong) mechanism, with formation of a covalent intermediate. Several steps of catalysis by EcAII are unique when compared to reactions catalyzed by other known hydrolytic enzymes. Here, the reaction is initiated by a weak nucleophile, threonine, without direct assistance of a general base, although a distant general base is identified. Furthermore, tetrahedral intermediates formed during the catalytic process are stabilized by a never previously described motif. Although the scheme of the catalytic mechanism was developed only on the basis of data obtained from EcAII and its variants, this novel mechanism of enzymatic hydrolysis could potentially apply to most (and possibly all) l-asparaginases. PubMed: 32364696DOI: 10.1021/acs.biochem.0c00116 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.95 Å) |
Structure validation
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