5K4H

Wolinella succinogenes L-asparaginase S121 + L-Glutamic acid

Summary for 5K4H

• Entry DOI: 10.2210/pdb5k4h/pdb
• Related: 5K3O 5K45 5K4G
• Descriptor: L-asparaginase, GLUTAMIC ACID (3 entities in total)
• Functional Keywords: l-asparaginase, s121, l-glutamic acid, hydrolase
• Biological source: Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W)
• Cellular location: Cytoplasm: P50286
• Total number of polymer chains: 8
• Total formula weight: 280326.66

Authors

Nguyen, H.A.,Lave, A. (deposition date: 2016-05-20, release date: 2017-03-29, Last modification date: 2023-09-27)

Primary citation

Nguyen, H.A.,Durden, D.L.,Lavie, A.
The differential ability of asparagine and glutamine in promoting the closed/active enzyme conformation rationalizes the Wolinella succinogenes L-asparaginase substrate specificity.
Sci Rep, 7:41643-41643, 2017

PubMed Abstract: Many side effects of current FDA-approved L-asparaginases have been related to their secondary L-glutaminase activity. The Wolinella succinogenes L-asparaginase (WoA) has been reported to be L-glutaminase free, suggesting it would have fewer side effects. Unexpectedly, the WoA variant with a proline at position 121 (WoA-P) was found to have L-glutaminase activity in contrast to Uniprot entry P50286 (WoA-S) that has a serine residue at this position. Towards understanding how this residue impacts the L-glutaminase property, kinetic analysis was coupled with crystal structure determination of these WoA variants. WoA-S was confirmed to have much lower L-glutaminase activity than WoA-P, yet both showed comparable L-asparaginase activity. Structures of the WoA variants in complex with L-aspartic acid versus L-glutamic acid provide insights into their differential substrate selectivity. Structural analysis suggests a mechanism by which residue 121 impacts the conformation of the conserved tyrosine 27, a component of the catalytically-important flexible N-terminal loop. Surprisingly, we could fully model this loop in either its open or closed conformations, revealing the roles of specific residues of an evolutionary conserved motif among this L-asparaginase family. Together, this work showcases critical residues that influence the ability of the flexible N-terminal loop for adopting its active conformation, thereby effecting substrate specificity.

PubMed: 28139703
DOI: 10.1038/srep41643

Experimental method

X-RAY DIFFRACTION (2 Å)