8HVQ | pdb_00008hvq

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

PDB DOI: https://doi.org/10.2210/pdb8HVQ/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus lugdunensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-12-27 Released: 2023-12-27
Deposition Author(s): Kaur, H., Mahto, J.K., Kumar, P., Sharma, A.K.
Funding Organization(s): Department of Science & Technology (DST, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.199 (Depositor), 0.203 (DCC)
R-Value Work:
0.151 (Depositor)
R-Value Observed:
0.153 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Characterization of haloacid dehalogenase superfamily acid phosphatase from Staphylococcus lugdunensis.

Kaur, H., Rode, S., Kp, S., Mahto, J.K., Alam, M.S., Gupta, D.N., Kar, B., Singla, J., Kumar, P., Sharma, A.K.

(2024) Arch Biochem Biophys 753: 109888-109888

PubMed: 38232797 Search on PubMed
DOI: https://doi.org/10.1016/j.abb.2024.109888
Primary Citation Related Structures:
8HVQ

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.

Organizational Affiliation

Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India.

Macromolecule Content

Total Structure Weight: 53.13 kDa
Atom Count: 4,392
Modeled Residue Count: 460
Deposited Residue Count: 466
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cof-type HAD-IIB family hydrolase	A, B	233	Staphylococcus lugdunensis	Mutation(s): 0 Gene Names: EQ812_11540
UniProt
Find proteins for A0A292DKY6 (Staphylococcus lugdunensis) Explore A0A292DKY6 Go to UniProtKB: A0A292DKY6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A292DKY6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
OXM Query on OXM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	OXAMIC ACID C₂ H₃ N O₃ SOWBFZRMHSNYGE-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	D [auth A], G [auth A], H [auth B], J [auth B], K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth B] Focus chain K [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]