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Conformational changes of loops highlight a potential binding site in Rhodococcus equi VapB
Author(s) -
Geerds Christina,
Haas Albert,
Niemann Hartmut H.
Publication year - 2021
Publication title -
acta crystallographica section f
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.572
H-Index - 37
ISSN - 2053-230X
DOI - 10.1107/s2053230x2100738x
Subject(s) - antiparallel (mathematics) , barrel (horology) , binding site , protein structure , biophysics , ligand (biochemistry) , stereochemistry , chemistry , crystallography , molecule , biology , receptor , biochemistry , materials science , physics , organic chemistry , quantum mechanics , magnetic field , composite material
Virulence‐associated proteins (Vaps) contribute to the virulence of the pathogen Rhodococcus equi , but their mode of action has remained elusive. All Vaps share a conserved core of about 105 amino acids that folds into a compact eight‐stranded antiparallel β‐barrel with a unique topology. At the top of the barrel, four loops connect the eight β‐strands. Previous Vap structures did not show concave surfaces that might serve as a ligand‐binding site. Here, the structure of VapB in a new crystal form was determined at 1.71 Å resolution. The asymmetric unit contains two molecules. In one of them, the loop regions at the top of the barrel adopt a different conformation from other Vap structures. An outward movement of the loops results in the formation of a hydrophobic cavity that might act as a ligand‐binding site. This lends further support to the hypothesis that the structural similarity between Vaps and avidins suggests a potential binding function for Vaps.