8BI3
Structure of E. coli Class 2 L-asparaginase EcAIII, mutant M200W (crystal M200W#1)
This is a non-PDB format compatible entry.
Summary for 8BI3
| Entry DOI | 10.2210/pdb8bi3/pdb |
| Descriptor | Isoaspartyl peptidase subunit alpha, Isoaspartyl peptidase subunit beta, DI(HYDROXYETHYL)ETHER, ... (9 entities in total) |
| Functional Keywords | l-asparaginase, isoaspartylpeptidase, mutation, ntn-hydrolase, hydrolase |
| Biological source | Escherichia coli K-12 More |
| Total number of polymer chains | 4 |
| Total formula weight | 67986.64 |
| Authors | Sciuk, A.,Ruszkowski, M.,Jaskolski, M.,Loch, J.I. (deposition date: 2022-11-01, release date: 2023-05-03, Last modification date: 2024-02-07) |
| Primary citation | Janicki, M.,Sciuk, A.,Zielezinski, A.,Ruszkowski, M.,Ludwikow, A.,Karlowski, W.M.,Jaskolski, M.,Loch, J.I. The effects of nature-inspired amino acid substitutions on structural and biochemical properties of the E. coli L-asparaginase EcAIII. Protein Sci., 32:e4647-e4647, 2023 Cited by PubMed Abstract: The Escherichia coli enzyme EcAIII catalyzes the hydrolysis of L-Asn to L-Asp and ammonia. Using a nature-inspired mutagenesis approach, we designed and produced five new EcAIII variants (M200I, M200L, M200K, M200T, M200W). The modified proteins were characterized by spectroscopic and crystallographic methods. All new variants were enzymatically active, confirming that the applied mutagenesis procedure has been successful. The determined crystal structures revealed new conformational states of the EcAIII molecule carrying the M200W mutation and allowed a high-resolution observation of an acyl-enzyme intermediate with the M200L mutant. In addition, we performed structure prediction, substrate docking, and molecular dynamics simulations for 25 selected bacterial orthologs of EcAIII, to gain insights into how mutations at the M200 residue affect the active site and substrate binding mode. This comprehensive strategy, including both experimental and computational methods, can be used to guide further enzyme engineering and can be applied to the study of other proteins of medicinal or biotechnological importance. PubMed: 37095066DOI: 10.1002/pro.4647 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.452 Å) |
Structure validation
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