6NXB

ECAII IN COMPLEX WITH CITRATE AT PH 7

Summary for 6NXB

• Entry DOI: 10.2210/pdb6nxb/pdb
• Related: 6nx6 6nx7 6nx8 6nx9 6nxa 6nxc 6nxd
• Descriptor: L-asparaginase 2, CITRIC ACID, GLYCEROL, ... (4 entities in total)
• Functional Keywords: hydrolysis of l-asparagine, hydrolase
• Biological source: Escherichia coli (strain K12)
• Total number of polymer chains: 4
• Total formula weight: 143400.23

Authors

Lubkowski, J.,Wlodawer, A. (deposition date: 2019-02-08, release date: 2019-08-07, Last modification date: 2019-11-20)

Primary citation

Lubkowski, J.,Chan, W.,Wlodawer, A.
Opportunistic complexes of E. coli L-asparaginases with citrate anions.
Sci Rep, 9:11070-11070, 2019

PubMed Abstract: Active sites of enzymes are highly optimized for interactions with specific substrates, thus binding of opportunistic ligands is usually observed only in the absence of native substrates or products. However, during growth of crystals required for structure determination enzymes are often exposed to conditions significantly divergent from the native ones, leading to binding of unexpected ligands to active sites even in the presence of substrates. Failing to recognize this possibility may lead to incorrect interpretation of experimental results and to faulty conclusions. Here, we present several examples of binding of a citrate anion to the active sites of E. coli L-asparaginases I and II, even in the presence of the native substrate, L-Asn. A part of this report focuses on a comprehensive re-interpretation of structural results published previously for complexes of type I L-asparaginase (EcAI) from E. coli. In two re-refined structures a citrate anion forms an acyl-enzyme reaction intermediate with the catalytic threonine. These results emphasize the importance of careful and critical analysis during interpretation of crystallographic data.

PubMed: 31363102
DOI: 10.1038/s41598-019-46432-0

Experimental method

X-RAY DIFFRACTION (1.75 Å)