6JV0 image
Entry Detail
PDB ID:
6JV0
Keywords:
Title:
Crystal Structure of N-terminal domain of ArgZ, bound to Product, an arginine dihydrolase from the Ornithine-Ammonia Cycle in Cyanobacteria
Biological Source:
PDB Version:
Deposition Date:
2019-04-15
Release Date:
2020-01-15
Method Details:
Experimental Method:
Resolution:
1.14 Å
R-Value Free:
0.19
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Sll1336 protein
Chain IDs:A
Chain Length:302
Number of Molecules:1
Biological Source:Synechocystis sp. (strain PCC 6803 / Kazusa)
Primary Citation
Crystal structures and biochemical analyses of the bacterial arginine dihydrolase ArgZ suggests a "bond rotation" catalytic mechanism.
J.Biol.Chem. 295 2113 2124 (2020)
PMID: 31914412 DOI: 10.1074/jbc.RA119.011752

Abstact

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 Synechocystis 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, Asn71, 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.

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