6LUH

High resolution structure of N(omega)-hydroxy-L-arginine hydrolase

Summary for 6LUH

• Entry DOI: 10.2210/pdb6luh/pdb
• Descriptor: N(omega)-hydroxy-L-arginine amidinohydrolase, MANGANESE (II) ION, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: hydrolase
• Biological source: Streptomyces lavendulae
• Total number of polymer chains: 2
• Total formula weight: 60277.46

Authors

Oda, K.,Matoba, Y. (deposition date: 2020-01-28, release date: 2020-09-02, Last modification date: 2025-03-12)

Primary citation

Oda, K.,Shimotani, N.,Kuroda, T.,Matoba, Y.
Crystal structure of an Nomega-hydroxy-L-arginine hydrolase found in the D-cycloserine biosynthetic pathway.
Acta Crystallogr D Struct Biol, 76:506-514, 2020

PubMed Abstract: DcsB, one of the enzymes encoded in the D-cycloserine (D-CS) biosynthetic gene cluster, displays a high sequence homology to arginase, which contains two manganese ions in the active site. However, DcsB hydrolyzes N-hydroxy-L-arginine, but not L-arginine, to supply hydroxyurea for the biosynthesis of D-CS. Here, the crystal structure of DcsB was determined at a resolution of 1.5 Å using anomalous scattering from the manganese ions. In the crystal structure, DscB generates an artificial dimer created by the open and closed forms. Gel-filtration analysis demonstrated that DcsB is a monomeric protein, unlike arginase, which forms a trimeric structure. The active center containing the binuclear manganese cluster differs between DcsB and arginase. In DcsB, one of the ligands of the Mn ion is a cysteine, while the corresponding residue in arginase is a histidine. In addition, DcsB has no counterpart to the histidine residue that acts as a general acid/base during the catalytic reaction of arginase. The present study demonstrates that DcsB has a unique active site that differs from that of arginase.

PubMed: 32496212
DOI: 10.1107/S2059798320004908

Experimental method

X-RAY DIFFRACTION (1.5 Å)