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The crystal structure of the TonB‐dependent transporter YncD reveals a positively charged substrate‐binding site
Author(s) -
Grinter Rhys,
Lithgow Trevor
Publication year - 2020
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.374
H-Index - 138
ISSN - 2059-7983
DOI - 10.1107/s2059798320004398
Subject(s) - gammaproteobacteria , bacterial outer membrane , transporter , escherichia coli , bacteria , periplasmic space , ferric , betaproteobacteria , biology , aerobactin , biochemistry , alphaproteobacteria , membrane transport protein , biophysics , binding site , chemistry , enterobacteriaceae , actinobacteria , inorganic chemistry , genetics , gene , 16s ribosomal rna
The outer membrane of Gram‐negative bacteria is highly impermeable to hydrophilic molecules of larger than 600 Da, protecting these bacteria from toxins present in the environment. In order to transport nutrients across this impermeable membrane, Gram‐negative bacteria utilize a diverse family of outer‐membrane proteins called TonB‐dependent transporters. The majority of the members of this family transport iron‐containing substrates. However, it is becoming increasingly clear that TonB‐dependent transporters target chemically diverse substrates. In this work, the structure and phylogenetic distribution of the TonB‐dependent transporter YncD are investigated. It is shown that while YncD is present in some enteropathogens, including Escherichia coli and Salmonella spp., it is also widespread in Gammaproteobacteria and Betaproteobacteria of environmental origin. The structure of YncD was determined, showing that despite a distant evolutionary relationship, it shares structural features with the ferric citrate transporter FecA, including a compact positively charged substrate‐binding site. Despite these shared features, it is shown that YncD does not contribute to the growth of E. coli in pure culture under iron‐limiting conditions or with ferric citrate as an iron source. Previous studies of transcriptional regulation in E. coli show that YncD is not induced under iron‐limiting conditions and is unresponsive to the ferric uptake regulator (Fur). These observations, combined with the data presented here, suggest that YncD is not responsible for the transport of an iron‐containing substrate.