8HVQ

Crystal structure of haloacid dehalogenase-like hydrolase family enzyme from Staphylococcus lugdunensis

Summary for 8HVQ

• Entry DOI: 10.2210/pdb8hvq/pdb
• Descriptor: Cof-type HAD-IIB family hydrolase, DI(HYDROXYETHYL)ETHER, 1,2-ETHANEDIOL, ... (6 entities in total)
• Functional Keywords: phosphatase, acidic ph, had family enzyme, staphylococcus, hydrolase
• Biological source: Staphylococcus lugdunensis
• Total number of polymer chains: 2
• Total formula weight: 53129.66

Authors

Kaur, H.,Mahto, J.K.,Kumar, P.,Sharma, A.K. (deposition date: 2022-12-27, release date: 2023-12-27, Last modification date: 2024-05-29)

Primary citation

Kaur, H.,Rode, S.,Kp, S.,Mahto, J.K.,Alam, M.S.,Gupta, D.N.,Kar, B.,Singla, J.,Kumar, P.,Sharma, A.K.
Characterization of haloacid dehalogenase superfamily acid phosphatase from Staphylococcus lugdunensis.
Arch.Biochem.Biophys., 753:109888-109888, 2024

PubMed Abstract: The haloacid dehalogenase superfamily implicated in bacterial pathogenesis comprises different enzymes having roles in many metabolic pathways. Staphylococcus lugdunensis, a Gram-positive bacterium, is an opportunistic human pathogen causing infections in the central nervous system, urinary tract, bones, peritoneum, systemic conditions and cutaneous infection. The haloacid dehalogenase superfamily proteins play a significant role in the pathogenicity of certain bacteria, facilitating invasion, survival, and proliferation within host cells. The genome of S. lugdunensis encodes more than ten proteins belonging to this superfamily. However, none of them have been characterized. The present work reports the characterization of one of the haloacid dehalogenase superfamily proteins (SLHAD1) from Staphylococcus lugdunensis. The functional analysis revealed that SLHAD1 is a metal-dependent acid phosphatase, which catalyzes the dephosphorylation of phosphorylated metabolites of cellular pathways, including glycolysis, gluconeogenesis, nucleotides, and thiamine metabolism. Based on the substrate specificity and genomic analysis, the physiological function of SLHAD1 in thiamine metabolism has been tentatively assigned. The crystal structure of SLHAD1, lacking 49 residues at the C-terminal, was determined at 1.7 Å resolution with a homodimer in the asymmetric unit. It was observed that SLHAD1 exhibited time-dependent cleavage at a specific point, occurring through a self-initiated process. A combination of bioinformatics, biochemical, biophysical, and structural studies explored unique features of SLHAD1. Overall, the study revealed a detailed characterization of a critical enzyme of the human pathogen Staphylococcus lugdunensis, associated with several life-threatening infections.

PubMed: 38232797
DOI: 10.1016/j.abb.2024.109888

Experimental method

X-RAY DIFFRACTION (1.73 Å)