6JUZ

Crystal Structure of N-terminal domain of ArgZ(N71S) covalently bond to a reaction intermediate

Summary for 6JUZ

• Entry DOI: 10.2210/pdb6juz/pdb
• Descriptor: Sll1336 protein, ARGININE, 1,2-ETHANEDIOL, ... (4 entities in total)
• Functional Keywords: arginine dihydrolase, amidino-transferase domain, alpha/beta propeller fold, (lor/sdh superfamily), hydrolase
• Biological source: Synechocystis sp. (strain PCC 6803 / Kazusa)
• Total number of polymer chains: 1
• Total formula weight: 35345.30

Authors

Zhuang, N.,Li, L.,Wu, X.,Zhuang, Y. (deposition date: 2019-04-15, release date: 2020-01-15, Last modification date: 2023-11-22)

Primary citation

Zhuang, N.,Zhang, H.,Li, L.,Wu, X.,Yang, C.,Zhang, Y.
Crystal structures and biochemical analyses of the bacterial arginine dihydrolase ArgZ suggests a "bond rotation" catalytic mechanism.
J.Biol.Chem., 295:2113-2124, 2020

PubMed Abstract: A recently discovered ornithine-ammonia cycle (OAC) serves as a conduit in the nitrogen storage and remobilization machinery in cyanobacteria. The OAC involves an arginine catabolic reaction catalyzed by the arginine dihydrolase ArgZ whose catalytic mechanism is unknown. Here we determined the crystal structures at 1.2-3.0 Å of unliganded ArgZ from the cyanobacterium sp. PCC6803 and of ArgZ complexed with its substrate arginine, a covalently linked reaction intermediate, or the reaction product ornithine. The structures reveal that a key residue, Asn, in the ArgZ active center functions as the determinant distinguishing ArgZ from other members of the guanidino group-modifying enzyme superfamily. The structures, along with biochemical evidence from enzymatic assays coupled with electrospray ionization MS techniques, further suggest that ArgZ-catalyzed conversion of arginine to ornithine, ammonia, and carbon dioxide consists of two successive cycles of amine hydrolysis. Finally, we show that arginine dihydrolases are broadly distributed among bacteria and metazoans, suggesting that the OAC may be frequently used for redistribution of nitrogen from arginine catabolism or nitrogen fixation.

PubMed: 31914412
DOI: 10.1074/jbc.RA119.011752

Experimental method

X-RAY DIFFRACTION (1.21 Å)