7ARP

Native L-2-haloacid dehalogenase from Zobellia galactanivorans

Summary for 7ARP

• Entry DOI: 10.2210/pdb7arp/pdb
• Descriptor: (S)-2-haloacid dehalogenase, PHOSPHATE ION, THIOCYANATE ION, ... (4 entities in total)
• Functional Keywords: haloacid dehalogenase, rossmann fold, cytoplasmic, hydrolase
• Biological source: Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij)
• Total number of polymer chains: 2
• Total formula weight: 53058.89

Authors

Grigorian, E.,Roret, T.,Czjzek, M.,Leblanc, C.,Delage, L. (deposition date: 2020-10-26, release date: 2021-09-08, Last modification date: 2024-01-31)

Primary citation

Grigorian, E.,Roret, T.,Czjzek, M.,Leblanc, C.,Delage, L.
X-ray structure and mechanism of ZgHAD, a L-2-haloacid dehalogenase from the marine Flavobacterium Zobellia galactanivorans.
Protein Sci., :e4540-e4540, 2022

PubMed Abstract: Haloacid dehalogenases are potentially involved in bioremediation of contaminated environments and few have been biochemically characterized from marine organisms. The l-2-haloacid dehalogenase (l-2-HAD) from the marine Bacteroidetes Zobellia galactanivorans Dsij (ZgHAD) has been shown to catalyze the dehalogenation of C2 and C3 short-chain l-2-haloalkanoic acids. To better understand its catalytic properties, its enzymatic stability, active site, and 3D structure were analyzed. ZgHAD demonstrates high stability to solvents and a conserved catalytic activity when heated up to 60°C, its melting temperature being at 65°C. The X-ray structure of the recombinant enzyme was solved by molecular replacement. The enzyme folds as a homodimer and its active site is very similar to DehRhb, the other known l-2-HAD from a marine Rhodobacteraceae. Marked differences are present in the putative substrate entrance sites of the two enzymes. The H179 amino acid potentially involved in the activation of a catalytic water molecule was confirmed as catalytic amino acid through the production of two inactive site-directed mutants. The crystal packing of 13 dimers in the asymmetric unit of an active-site mutant, ZgHAD-H179N, reveals domain movements of the monomeric subunits relative to each other. The involvement of a catalytic His/Glu dyad and substrate binding amino acids was further confirmed by computational docking. All together our results give new insights into the catalytic mechanism of the group of marine l-2-HAD.

PubMed: 36502283
DOI: 10.1002/pro.4540

Experimental method

X-RAY DIFFRACTION (1.78 Å)