5F9Q | pdb_00005f9q

Crystal structure of the extracellular domain of noncanonic ABC-type transporter YknZ from Gram-positive bacteria

• PDB DOI: https://doi.org/10.2210/pdb5F9Q/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Bacillus amyloliquefaciens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-12-10 Released: 2016-02-03 
• Deposition Author(s): Xu, Y., Guo, J., Jiang, R., Jin, X., Fan, S., Quan, C.S., Ha, N.C.
• Funding Organization(s): the National Natural Science Foundation of China, China Postdoctoral Science Foundation, the Fundamental Research Funds for the Central Universities

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

The Crystal Structure of the YknZ Extracellular Domain of ABC Transporter YknWXYZ from Bacillus amyloliquefaciens.

Xu, Y., Guo, J., Wang, L., Jiang, R., Jin, X., Liu, J., Fan, S., Quan, C.S., Ha, N.C.

(2016) PLoS One 11: e0155846-e0155846

• PubMed: 27243566 
• DOI: https://doi.org/10.1371/journal.pone.0155846
• Primary Citation Related Structures: 
  5F9Q


• PubMed Abstract: 
  

  Bacillus possesses the peptide toxin Sporulation-Delaying Protein (SDP), which can kill cells within a biofilm to support continued growth, thereby delaying the onset of biofilm sporulation. The four-component transporter YknWXYZ acts as a major SDP efflux pump to protect cells against the endogenous SDP toxin, for which YknYZ is a non-canonical ATP-binding cassette (ABC)-type transporter. YknYZ consists of the following two components: (1) an individual protein (YknY) and (2) a respective permease (YknZ). To date, the crystal structure, molecular function, and mechanism of action of the integral membrane protein YknZ remain to be elucidated. In this study, to characterize the structural and biochemical roles of YknZ in the functional assembly of YknWXYZ, we predicted and overexpressed the YknZ extracellular domain. We determined the crystal structure of B. amyloliquefaciens YknZ at a resolution of 2.0 Å. The structure revealed that the YknZ extracellular region exhibits significant structural similarity with the MacB periplasmic domain, which is a non-canonical ABC-type transporter in the tripartite macrolide-specific efflux pump in Gram-negative bacteria. We also found that the YknZ extracellular domain can directly bind to an extracellular component of YknX. This structural and biochemical study provides insights into the assembly of YknWXYZ, which may be relevant to understanding cannibalistic peptide toxin resistance in Bacillus and controlling bacterial growth.

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Organizational Affiliation: 
• Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian 116600, Liaoning, China.
Laboratory of Biomedical Material Engineering, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China.
School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, Liaoning, China.
College of Life and Health Sciences, Northeastern University, Shenyang 110004, Liaoning, China.
Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 22.08 kDa 
• Atom Count: 1,530 
• Modeled Residue Count: 187 
• Deposited Residue Count: 199 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrolide export ATP-binding/permease protein YknZ	A	199	Bacillus amyloliquefaciens	Mutation(s): 0  Gene Names: ABH13_1432

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.169	α = 90
b = 46.147	β = 90
c = 87.543	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Xu, Y., Guo, J., Jiang, R., Jin, X., Fan, S., Quan, C.S., Ha, N.C.

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Funding Organization	Location	Grant Number
the National Natural Science Foundation of China	China	31200556
the National Natural Science Foundation of China	China	21402024
the National Natural Science Foundation of China	China	21272031
China Postdoctoral Science Foundation	China	2013M540229
the Fundamental Research Funds for the Central Universities	China	DC201502020203

Revision History  

• Version 1.0: 2016-02-03
  Type: Initial release
  
• Version 1.1: 2016-09-14
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary