6K1T | pdb_00006k1t

The structure of Francisella virulence factor BioJ

• PDB DOI: https://doi.org/10.2210/pdb6K1T/pdb

• Classification: HYDROLASE
• Organism(s): Francisella philomiragia subsp. philomiragia ATCC 25015
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-12 Released: 2020-04-15 
• Deposition Author(s): Ouyang, S., Guan, H., Zhang, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.235 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Molecular Basis of BioJ, a Unique Gatekeeper in Bacterial Biotin Synthesis.

Wei, W., Guan, H., Zhu, T., Zhang, S., Fan, C., Ouyang, S., Feng, Y.

(2019) iScience 19: 796-808

• PubMed: 31494495 
• DOI: https://doi.org/10.1016/j.isci.2019.08.028
• Primary Citation Related Structures: 
  6K1T


• PubMed Abstract: 
  

  Biotin is an indispensable cofactor in the three domains of life. The unusual virulence factor BioJ of Francisella catalyzes the formation of pimeloyl-ACP, an intermediate in biotin synthesis. Here, we report the 1.58 Å crystal structure of BioJ, the enzymatic activity of which is determined with the in vitro reconstituted reaction and biotin bioassay in vivo. Unlike the paradigm BioH, BioJ displays an atypical α/β-hydrolase fold. A structurally conserved catalytic triad (S151, D248, and H278) of BioJ is functionally defined. A proposed model for BioJ catalysis involves two basic residues-rich cavities, of which cavity-1, rather than cavity-2, binds to the ACP moiety of its physiological substrate, pimeloyl-ACP methyl ester. In summary, this finding provides molecular insights into the BioJ gatekeeper of biotin synthesis.

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Organizational Affiliation: 
• Department of Pathogen Biology & Microbiology and General Intensive Care Unit of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; College of Animal Science, Zhejiang University, Hangzhou 310058, China.
The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China.
CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China.
The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China. Electronic address: [e-mail].
Department of Pathogen Biology & Microbiology and General Intensive Care Unit of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; College of Animal Science, Zhejiang University, Hangzhou 310058, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.48 kDa 
• Atom Count: 2,659 
• Modeled Residue Count: 299 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha/beta hydrolase fold family protein	A	306	Francisella philomiragia subsp. philomiragia ATCC 25015	Mutation(s): 0  Gene Names: BZ13_192

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.235 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.943	α = 90
b = 67.313	β = 112.55
c = 55.571	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data collection
autoPROC	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-15 
Deposition Author(s): Ouyang, S., Guan, H., Zhang, S.

Revision History  

• Version 1.0: 2020-04-15
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Refinement description