7CD4 image
Deposition Date 2020-06-18
Release Date 2021-03-03
Last Version Date 2024-10-16
Entry Detail
PDB ID:
7CD4
Title:
Crystal structure of the S103F mutant of Bacillus subtilis (natto) YabJ protein.
Biological Source:
Method Details:
Experimental Method:
Resolution:
2.10 Å
R-Value Free:
0.22
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:YabJ protein
Mutations:S103F
Chain IDs:A, B, C, D
Chain Length:125
Number of Molecules:4
Biological Source:Bacillus subtilis subsp. natto (strain BEST195)
Primary Citation
Tetramer formation of Bacillus subtilis YabJ protein that belongs to YjgF/YER057c/UK114 family.
Biosci.Biotechnol.Biochem. 85 297 306 (2021)
PMID: 33590041 DOI: 10.1093/bbb/zbaa037

Abstact

Bacillus subtilis YabJ protein belongs to the highly conserved YjgF/YER057c/UK114 family, which has a homotrimeric quaternary structure. The dominant allele of yabJ gene that is caused by a single amino acid mutation of Ser103Phe enables poly-γ-glutamic acid (γPGA) production of B. subtilis under conditions where the cell-density signal transduction was disturbed by the loss of DegQ function. X-ray crystallography of recombinant proteins revealed that unlike the homotrimeric wild-type YabJ, the mutant YabJ(Ser103Phe) had a homotetrameric quaternary structure, and the structural change appeared to be triggered by an inversion of the fifth β-strand. The YabJ homotetramer has a hole that is highly accessible, penetrating through the tetramer, and 2 surface concaves as potential ligand-binding sites. Western blot analyses revealed that the conformational change was also induced in vivo by the Ser103Phe mutation.

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