8EC4

XFEL structure of Mycobacterium tuberculosis beta lactamase microcrystals mixed with sulbactam for 240ms

Summary for 8EC4

• Entry DOI: 10.2210/pdb8ec4/pdb
• Descriptor: Beta-lactamase, PHOSPHATE ION, TRANS-ENAMINE INTERMEDIATE OF SULBACTAM, ... (4 entities in total)
• Functional Keywords: beta lactamase, sulbactam, inhibitor, hydrolase, hydrolase-inhibitor complex, hydrolase/inhibitor
• Biological source: Mycobacterium tuberculosis
• Total number of polymer chains: 4
• Total formula weight: 114924.32

Authors

Malla, T.N.,Schmidt, M. (deposition date: 2022-09-01, release date: 2023-03-08, Last modification date: 2023-10-25)

Primary citation

Malla, T.N.,Zielinski, K.,Aldama, L.,Bajt, S.,Feliz, D.,Hayes, B.,Hunter, M.,Kupitz, C.,Lisova, S.,Knoska, J.,Martin-Garcia, J.M.,Mariani, V.,Pandey, S.,Poudyal, I.,Sierra, R.G.,Tolstikova, A.,Yefanov, O.,Yoon, C.H.,Ourmazd, A.,Fromme, P.,Schwander, P.,Barty, A.,Chapman, H.N.,Stojkovic, E.A.,Batyuk, A.,Boutet, S.,Phillips Jr., G.N.,Pollack, L.,Schmidt, M.
Heterogeneity in M. tuberculosis beta-lactamase inhibition by Sulbactam.
Nat Commun, 14:5507-5507, 2023

PubMed Abstract: For decades, researchers have elucidated essential enzymatic functions on the atomic length scale by tracing atomic positions in real-time. Our work builds on possibilities unleashed by mix-and-inject serial crystallography (MISC) at X-ray free electron laser facilities. In this approach, enzymatic reactions are triggered by mixing substrate or ligand solutions with enzyme microcrystals. Here, we report in atomic detail (between 2.2 and 2.7 Å resolution) by room-temperature, time-resolved crystallography with millisecond time-resolution (with timepoints between 3 ms and 700 ms) how the Mycobacterium tuberculosis enzyme BlaC is inhibited by sulbactam (SUB). Our results reveal ligand binding heterogeneity, ligand gating, cooperativity, induced fit, and conformational selection all from the same set of MISC data, detailing how SUB approaches the catalytic clefts and binds to the enzyme noncovalently before reacting to a trans-enamine. This was made possible in part by the application of singular value decomposition to the MISC data using a program that remains functional even if unit cell parameters change up to 3 Å during the reaction.

PubMed: 37679343
DOI: 10.1038/s41467-023-41246-1

Experimental method

X-RAY DIFFRACTION (2.35 Å)