5H8J

Crystal structure of Medicago truncatula N-carbamoylputrescine amidohydrolase (MtCPA) in complex with cadaverine

Summary for 5H8J

• Entry DOI: 10.2210/pdb5h8j/pdb
• Related: 5H8I 5H8K 5H8L
• Descriptor: N-carbamoylputrescine amidohydrolase, GLYCEROL, DI(HYDROXYETHYL)ETHER, ... (7 entities in total)
• Functional Keywords: amidase, helical octamer, alpha-beta-beta-alpha sandwich fold, putrescine biosynthesis, hydrolase
• Biological source: Medicago truncatula (Barrel medic)
• Total number of polymer chains: 16
• Total formula weight: 550646.19

Authors

Sekula, B.,Ruszkowski, M.,Malinska, M.,Dauter, Z. (deposition date: 2015-12-23, release date: 2016-04-20, Last modification date: 2023-09-27)

Primary citation

Sekula, B.,Ruszkowski, M.,Malinska, M.,Dauter, Z.
Structural Investigations of N-carbamoylputrescine Amidohydrolase from Medicago truncatula: Insights into the Ultimate Step of Putrescine Biosynthesis in Plants.
Front Plant Sci, 7:350-350, 2016

PubMed Abstract: Putrescine, 1,4-diaminobutane, is an intermediate in the biosynthesis of more complexed polyamines, spermidine and spermine. Unlike other eukaryotes, plants have evolved a multistep pathway for putrescine biosynthesis that utilizes arginine. In the final reaction, N-carbamoylputrescine is hydrolyzed to putrescine by N-carbamoylputrescine amidohydrolase (CPA, EC 3.5.1.53). During the hydrolysis, consecutive nucleophilic attacks on the substrate by Cys158 and water lead to formation of putrescine and two by-products, ammonia and carbon dioxide. CPA from the model legume plant, Medicago truncatula (MtCPA), was investigated in this work. Four crystal structures were determined: the wild-type MtCPA in complex with the reaction intermediate, N-(dihydroxymethyl)putrescine as well as with cadaverine, which is a longer analog of putrescine; and also structures of MtCPA-C158S mutant unliganded and with putrescine. MtCPA assembles into octamers, which resemble an incomplete left-handed helical twist. The active site of MtCPA is funnel-like shaped, and its entrance is walled with a contribution of the neighboring protein subunits. Deep inside the catalytic cavity, Glu48, Lys121, and Cys158 form the catalytic triad. In this studies, we have highlighted the key residues, highly conserved among the plant kingdom, responsible for the activity and selectivity of MtCPA toward N-carbamoylputrescine. Moreover, since, according to previous reports, a close MtCPA relative from Arabidopsis thaliana, along with several other nitrilase-like proteins, are subjected to allosteric regulation by substrates, we have used the structural information to indicate a putative secondary binding site. Based on the docking experiment, we postulate that this site is adjacent to the entrance to the catalytic pocket.

PubMed: 27066023
DOI: 10.3389/fpls.2016.00350

Experimental method

X-RAY DIFFRACTION (2.19 Å)