Substrate flexibility of the catechol siderophore periplasmic binding proteins, RupB and YiuA from Yersinia ruckeri YRB

ABSTRACT

Bacteria often produce siderophores - small molecules with high affinity for Fe(III) - to acquire the iron that they need to grow. After transport of the Fe(III)-siderophore across the outer membrane of Gram-negative bacteria, a periplasmic binding protein (PBP) generally shuttles the Fe(III)-siderophore through the periplasm to the inner membrane. The fish pathogen Yersinia ruckeri synthesizes the oligoester tris-catecholate siderophore ruckerbactin, (DHB-LArg-LSer)3 (1), to acquire iron during infection. Its biosynthetic gene cluster encodes a single PBP, RupB, which was presumed to bind Fe(III)-ruckerbactin, however, previous fluorescence quenching titrations revealed RupB does not bind Fe(III)-ruckerbactin nor the Fe(III) complexes of its hydrolysis products - the bis- and mono-catecholate siderophores, 2 and 3, respectively - with biologically relevant affinities. Instead, RupB binds the complex of the structurally-related siderophore enterobactin, (DHB-LSer)3, which is surprising since enterobactin is not biosynthesized by Y. ruckeri. RupB inverts the chirality of the Δ-Fe(III)-enterobactin to Λ upon binding. A second PBP, YiuA, which is encoded elsewhere in the genome was established previously to bind the 1:2 Fe(III) complex of the mono-catecholate DHB-LArg-LSer (3), Fe(III)-(3)2, as well as the diastereomeric complex Fe(III)-(4)2 with nanomolar affinities, in which 4 is the monocatechol DHB-DArg-LSer. We show that YiuA recognizes similar siderophore scaffolds containing the alternative cationic amino acids (Lys, Orn), suggesting a broader role in xenosiderophore uptake. YiuA binds its substrate in the Λ isomer regardless of the chirality of the complex presented to it.