6VSU

Arginase from Arabidopsis thaliana in Complex with Ornithine

Summary for 6VSU

• Entry DOI: 10.2210/pdb6vsu/pdb
• Descriptor: Arginase 1, mitochondrial, MANGANESE (II) ION, SODIUM ION, ... (7 entities in total)
• Functional Keywords: arginine amidinohydrolase; ureohydrolase; agmatinase; agmatine amidinohydrolase, hydrolase
• Biological source: Arabidopsis thaliana (Mouse-ear cress)
• Total number of polymer chains: 24
• Total formula weight: 846681.56

Authors

Sekula, B. (deposition date: 2020-02-11, release date: 2020-08-12, Last modification date: 2023-10-11)

Primary citation

Sekula, B.
The Neighboring Subunit Is Engaged to Stabilize the Substrate in the Active Site of Plant Arginases.
Front Plant Sci, 11:987-987, 2020

PubMed Abstract: Arginine acts as a precursor of polyamines in plants in two known pathways, agmatine and ornithine routes. It is decarboxylated to agmatine by arginine decarboxylase, and then transformed to putrescine by the consecutive action of agmatine iminohydrolase and N-carbamoylputrescine amidohydrolase. Alternatively, it can be hydrolyzed to ornithine by arginase and then decarboxylated by ornithine decarboxylase to putrescine. Some plants lack a functional ornithine pathway, but all have one or two arginases that can have dual cellular localization, in mitochondria and plastids. It was recently shown that arginases from and soybean act also as agmatinases, thus they can produce putrescine directly from agmatine. Therefore, arginase (together with arginine decarboxylase) can complement putrescine production in plastids, providing a third polyamine biosynthesis pathway in plants. Phylogenetic analysis suggests that arginases, highly conserved in the plant kingdom, create the only group of enzymes recognized in the family of ureohydrolases in plants. Arginases are metalloenzymes with binuclear manganese cluster in the active site. In this work, two arginases from and are structurally characterized and their binding properties are discussed. Crystal structures with bound ornithine show that plant hexameric arginases engage a long loop from the neighboring subunit to stabilize α-amino and carboxyl groups of the ligand. This unique ligand binding mode is unobserved in arginases from other domains of life. Structural analysis shows that substrate binding by residues from two neighboring subunits might also characterize some prokaryotic agmatinases. This feature of plant arginases is most likely the determinant of their ability to recognize not only arginine but also agmatine as their substrates, thus, to act as arginase and agmatinase.

PubMed: 32754173
DOI: 10.3389/fpls.2020.00987

Experimental method

X-RAY DIFFRACTION (2.25 Å)