8K7P | pdb_00008k7p

Staphylococcus aureus lipase -PSA complex

PDB DOI: https://doi.org/10.2210/pdb8K7P/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-07-27 Released: 2024-06-05
Deposition Author(s): Kitadokoro, J., Kamitani, S., Kitadokoro, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.218 (Depositor), 0.219 (DCC)
R-Value Work:
0.198 (Depositor), 0.199 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Staphylococcus aureus lipase complex with unsaturated petroselinic acid.

Kitadokoro, J., Kamitani, S., Okuno, Y., Hikima, T., Yamamoto, M., Hirokawa, T., Kitadokoro, K.

(2024) FEBS Open Bio 14: 942-954

PubMed: 38757397 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/2211-5463.13808
Primary Citation Related Structures:
8K7P, 8K7Q, 8YIB

PubMed Abstract:
Staphylococcus aureus produces large amounts of toxins and virulence factors. In patients with underlying diseases or compromised immune systems, this bacterium can lead to severe infections and potentially death. In this study, the crystal structure of the complex of S. aureus lipase (SAL), which is involved in the growth of this bacterium, with petroselinic acid (PSA), an inhibitor of unsaturated fatty acids, was determined by X-ray crystallography. Recently, PSA was shown to inhibit S. aureus biofilm formation and the enzymatic activity of SAL. To further characterize the inhibitory mechanism, we determined the half-inhibitory concentration of SAL by PSA and the crystal structure of the complex. The IC ₅₀ of the inhibitory effect of PSA on SAL was 3.4 μm. SAL and PSA inhibitors were co-crystallized, and diffraction data sets were collected to 2.19 Å resolution at SPring-8 to determine the crystal structure and elucidate the detailed structural interactions. The results show that the fatty acid moiety of PSA is tightly bound to a hydrophobic pocket extending in two directions around the catalytic residue Ser116. Ser116 was also covalently bonded to the carbon of the unsaturated fatty acid moiety, and an oxyanion hole in SAL stabilized the electrons of the double bond. The difference in inhibitory activity between PSA and ester compounds revealed a structure-activity relationship between SAL and PSA. Additional research is required to further characterize the clinical potential of PSA.

Organizational Affiliation

Faculty of Molecular Chemistry and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Japan.

Macromolecule Content

Total Structure Weight: 94.89 kDa
Atom Count: 6,394
Modeled Residue Count: 764
Deposited Residue Count: 816
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase 2	A, B	408	Staphylococcus aureus	Mutation(s): 0 Gene Names: lip, BN1321_80040 EC: 3.1.1.3
UniProt
Find proteins for A0A0U1MWF9 (Staphylococcus aureus) Explore A0A0U1MWF9 Go to UniProtKB: A0A0U1MWF9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0U1MWF9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 13 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4I1 (Subject of Investigation/LOI) Query on 4I1 Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain H [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain H [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain H [auth A]	BA [auth B], H [auth A]	Petroselinic acid C₁₈ H₃₄ O₂ CNVZJPUDSLNTQU-SEYXRHQNSA-N		Interactions Focus chain BA [auth B] Focus chain H [auth A] Interactions & Density Focus chain BA [auth B] Focus chain H [auth A]
DAO Query on DAO Download:Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain I [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain I [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain I [auth A]	GA [auth B], I [auth A]	LAURIC ACID C₁₂ H₂₄ O₂ POULHZVOKOAJMA-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain I [auth A] Interactions & Density Focus chain GA [auth B] Focus chain I [auth A]
OCA Query on OCA Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain E [auth A] SDF format, chain Z [auth B] SDF format, chain D [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain D [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain D [auth A]	AA [auth B], D [auth A], E [auth A], Z [auth B]	OCTANOIC ACID (CAPRYLIC ACID) C₈ H₁₆ O₂ WWZKQHOCKIZLMA-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain Z [auth B]
6NA Query on 6NA Download:Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain U [auth B] SDF format, chain X [auth B] SDF format, chain J [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain U [auth B] MOL2 format, chain X [auth B] MOL2 format, chain J [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain U [auth B] mmCIF format, chain X [auth B] mmCIF format, chain J [auth A]	HA [auth B], J [auth A], U [auth B], X [auth B]	HEXANOIC ACID C₆ H₁₂ O₂ FUZZWVXGSFPDMH-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain J [auth A] Focus chain U [auth B] Focus chain X [auth B] Interactions & Density Focus chain HA [auth B] Focus chain J [auth A] Focus chain U [auth B] Focus chain X [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain MA [auth B] SDF format, chain T [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain T [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain T [auth A]	MA [auth B], T [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain MA [auth B] Focus chain T [auth A] Interactions & Density Focus chain MA [auth B] Focus chain T [auth A]
BUA Query on BUA Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain Y [auth B]	Y [auth B]	butanoic acid C₄ H₈ O₂ FERIUCNNQQJTOY-UHFFFAOYSA-N		Interactions Focus chain Y [auth B] Interactions & Density Focus chain Y [auth B]
PPI Query on PPI 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]	PROPANOIC ACID C₃ H₆ O₂ XBDQKXXYIPTUBI-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain KA [auth B] SDF format, chain R [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain R [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain R [auth A]	KA [auth B], R [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain KA [auth B] Focus chain R [auth A] Interactions & Density Focus chain KA [auth B] Focus chain R [auth A]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain K [auth A] SDF format, chain FA [auth B] SDF format, chain EA [auth B] SDF format, chain C [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain K [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain C [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain K [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain C [auth A]	C [auth A] CA [auth B] DA [auth B] EA [auth B] FA [auth B] C [auth A], CA [auth B], DA [auth B], EA [auth B], FA [auth B], K [auth A], L [auth A], M [auth A], N [auth A], V [auth B], W [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain C [auth A] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth B] Focus chain W [auth B]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain LA [auth B] SDF format, chain S [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain S [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain S [auth A]	LA [auth B], S [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain LA [auth B] Focus chain S [auth A] Interactions & Density Focus chain LA [auth B] Focus chain S [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	IA [auth B], JA [auth B], O [auth A], P [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain IA [auth B] Focus chain JA [auth B] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain IA [auth B] Focus chain JA [auth B] Focus chain O [auth A] Focus chain P [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]