5F9Q

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

Summary for 5F9Q

• Entry DOI: 10.2210/pdb5f9q/pdb
• Descriptor: Macrolide export ATP-binding/permease protein YknZ (2 entities in total)
• Functional Keywords: bacillus amyloliquefaciens, sdp transporter yknwxyz, respective permease yknz, membrane protein
• Biological source: Bacillus amyloliquefaciens
• Total number of polymer chains: 1
• Total formula weight: 22082.58

Authors

Xu, Y.,Guo, J.,Jiang, R.,Jin, X.,Fan, S.,Quan, C.S.,Ha, N.C. (deposition date: 2015-12-10, release date: 2016-02-03, Last modification date: 2024-10-23)

Primary citation

Xu, Y.,Guo, J.,Wang, L.,Jiang, R.,Jin, X.,Liu, J.,Fan, S.,Quan, C.S.,Ha, N.C.
The Crystal Structure of the YknZ Extracellular Domain of ABC Transporter YknWXYZ from Bacillus amyloliquefaciens.
Plos One, 11:e0155846-e0155846, 2016

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.

PubMed: 27243566
DOI: 10.1371/journal.pone.0155846

Experimental method

X-RAY DIFFRACTION (2.044 Å)