6SF7 | pdb_00006sf7

Atomic resolution structure of SplF protease from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb6SF7/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus subsp. aureus USA300
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-08-01 Released: 2021-03-03
Deposition Author(s): Golik, P., Stach, N., Karim, A., Dubin, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.208 (Depositor), 0.214 (DCC)
R-Value Work:
0.167 (Depositor), 0.176 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural Determinants of Substrate Specificity of SplF Protease from Staphylococcus aureus .

Stach, N., Karim, A., Golik, P., Kitel, R., Pustelny, K., Gruba, N., Groborz, K., Jankowska, U., Kedracka-Krok, S., Wladyka, B., Drag, M., Lesner, A., Dubin, G.

(2021) Int J Mol Sci 22

PubMed: 33672341 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/ijms22042220
Primary Citation Related Structures:
6SF7

PubMed Abstract:
Accumulating evidence suggests that six proteases encoded in the spl operon of a dangerous human pathogen, Staphylococcus aureus , may play a role in virulence. Interestingly, SplA, B, D, and E have complementary substrate specificities while SplF remains to be characterized in this regard. Here, we describe the prerequisites of a heterologous expression system for active SplF protease and characterize the enzyme in terms of substrate specificity and its structural determinants. Substrate specificity of SplF is comprehensively profiled using combinatorial libraries of peptide substrates demonstrating strict preference for long aliphatic sidechains at the P1 subsite and significant selectivity for aromatic residues at P3. The crystal structure of SplF was provided at 1.7 Å resolution to define the structural basis of substrate specificity of SplF. The obtained results were compared and contrasted with the characteristics of other Spl proteases determined to date to conclude that the spl operon encodes a unique extracellular proteolytic system.

Organizational Affiliation

Malopolska Center of Biotechnology, Jagiellonian University, 7a Gronostajowa St., 30-387 Krakow, Poland.

Macromolecule Content

Total Structure Weight: 90.01 kDa
Atom Count: 6,562
Modeled Residue Count: 789
Deposited Residue Count: 820
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease SplF	A, B, C, D	205	Staphylococcus aureus subsp. aureus USA300	Mutation(s): 0 Gene Names: splF, SAUSA300_1753 EC: 3.4.21
UniProt
Find proteins for Q2FFT4 (Staphylococcus aureus (strain USA300)) Explore Q2FFT4 Go to UniProtKB: Q2FFT4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2FFT4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain Q [auth C]	Q [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Interactions & Density Focus chain Q [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth B] F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], P [auth C], T [auth D], U [auth D], V [auth D], W [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C]	O [auth B], R [auth C], S [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C]