7W7H | pdb_00007w7h

S Suis FakA-FakB2 complex structure

• PDB DOI: https://doi.org/10.2210/pdb7W7H/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus suis 05ZYH33
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-12-04 Released: 2022-09-21 
• Deposition Author(s): Shi, Y., Zang, N., Lou, N., Xu, Y., Sun, J., Huang, M., Zhang, H., Lu, H., Zhou, C., Feng, Y.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.221 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structure and mechanism for streptococcal fatty acid kinase (Fak) system dedicated to host fatty acid scavenging.

Shi, Y., Zang, N., Lou, N., Xu, Y., Sun, J., Huang, M., Zhang, H., Lu, H., Zhou, C., Feng, Y.

(2022) Sci Adv 8: eabq3944-eabq3944

• PubMed: 36054360 
• DOI: https://doi.org/10.1126/sciadv.abq3944
• Primary Citation Related Structures: 
  7W7H


• PubMed Abstract: 
  

  Staphylococcus and Streptococcus , two groups of major human pathogens, are equipped with a fatty acid kinase (Fak) machinery to scavenge host fatty acids. The Fak complex is contains an ATP-binding subunit FakA, which interacts with varied FakB isoforms, and synthesizes acyl-phosphate from extracellular fatty acids. However, how FakA recognizes its FakB partners and then activates different fatty acids is poorly understood. Here, we systematically describe the Fak system from the zoonotic pathogen, Streptococcus suis . The crystal structure of SsFakA complexed with SsFakB2 was determined at 2.6 Å resolution. An in vitro system of Fak-PlsX (phosphate: acyl-ACP transacylase) was developed to track acyl-phosphate intermediate and its final product acyl-ACP. Structure-guided mutagenesis enabled us to characterize a mechanism for streptococcal FakA working with FakB partners engaged in host fatty acid scavenging. These findings offer a comprehensive description of the Fak kinase machinery, thus advancing the discovery of attractive targets against deadly infections with Streptococcus .

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Organizational Affiliation: 
• Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
Department of Toxicology, School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 150.92 kDa 
• Atom Count: 10,340 
• Modeled Residue Count: 1,355 
• Deposited Residue Count: 1,385 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted kinase related to dihydroxyacetone kinase	A, B	554	Streptococcus suis 05ZYH33	Mutation(s): 0  Gene Names: SSU05_1861

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein conserved in bacteria	C [auth E]	277	Streptococcus suis 05ZYH33	Mutation(s): 0  Gene Names: SSU05_1650

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLA (Subject of Investigation/LOI)	I [auth E]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
SO4	E [auth A], F [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)	D [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.221 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.749	α = 90
b = 107.749	β = 90
c = 398.999	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-21 
Deposition Author(s): Shi, Y., Zang, N., Lou, N., Xu, Y., Sun, J., Huang, M., Zhang, H., Lu, H., Zhou, C., Feng, Y.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History  

• Version 1.0: 2022-09-21
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description