8A53

Crystal structure of AtMCA-IIf C147A (metacaspase 9) from Arabidopsis thaliana

Summary for 8A53

• Entry DOI: 10.2210/pdb8a53/pdb
• Descriptor: Metacaspase-9, NITRATE ION (3 entities in total)
• Functional Keywords: metacaspase, cysteine protease, caspase-hemoglobinase fold, plant protein, hydrolase
• Biological source: Arabidopsis thaliana (thale cress)
• Total number of polymer chains: 4
• Total formula weight: 153688.20

Authors

Sabljic, I.,Stael, S.,Stahlberg, J.,Bozhkov, P. (deposition date: 2022-06-14, release date: 2023-05-31, Last modification date: 2024-05-01)

Primary citation

Stael, S.,Sabljic, I.,Audenaert, D.,Andersson, T.,Tsiatsiani, L.,Kumpf, R.P.,Vidal-Albalat, A.,Lindgren, C.,Vercammen, D.,Jacques, S.,Nguyen, L.,Njo, M.,Fernandez-Fernandez, A.D.,Beunens, T.,Timmerman, E.,Gevaert, K.,Van Montagu, M.,Stahlberg, J.,Bozhkov, P.V.,Linusson, A.,Beeckman, T.,Van Breusegem, F.
Structure-function study of a Ca 2+ -independent metacaspase involved in lateral root emergence.
Proc.Natl.Acad.Sci.USA, 120:e2303480120-e2303480120, 2023

PubMed Abstract: Metacaspases are part of an evolutionarily broad family of multifunctional cysteine proteases, involved in disease and normal development. As the structure-function relationship of metacaspases remains poorly understood, we solved the X-ray crystal structure of an type II metacaspase (AtMCA-IIf) belonging to a particular subgroup not requiring calcium ions for activation. To study metacaspase activity in plants, we developed an in vitro chemical screen to identify small molecule metacaspase inhibitors and found several hits with a minimal thioxodihydropyrimidine-dione structure, of which some are specific AtMCA-IIf inhibitors. We provide mechanistic insight into the basis of inhibition by the TDP-containing compounds through molecular docking onto the AtMCA-IIf crystal structure. Finally, a TDP-containing compound (TDP6) effectively hampered lateral root emergence in vivo, probably through inhibition of metacaspases specifically expressed in the endodermal cells overlying developing lateral root primordia. In the future, the small compound inhibitors and crystal structure of AtMCA-IIf can be used to study metacaspases in other species, such as important human pathogens, including those causing neglected diseases.

PubMed: 37216519
DOI: 10.1073/pnas.2303480120

Experimental method

X-RAY DIFFRACTION (1.95 Å)