6V81

The crystal structure of the outer-membrane transporter YncD

Summary for 6V81

• Entry DOI: 10.2210/pdb6v81/pdb
• Descriptor: Probable TonB-dependent receptor YncD, octyl beta-D-glucopyranoside, CALCIUM ION (3 entities in total)
• Functional Keywords: tonb-dependent transporter, membrane protein, outer membrane, gram-negative bacteria, transport protein
• Biological source: Escherichia coli BW25113
• Total number of polymer chains: 1
• Total formula weight: 77666.87

Authors

Grinter, R. (deposition date: 2019-12-10, release date: 2020-05-06, Last modification date: 2024-10-23)

Primary citation

Grinter, R.,Lithgow, T.
The crystal structure of the TonB-dependent transporter YncD reveals a positively charged substrate-binding site.
Acta Crystallogr D Struct Biol, 76:484-495, 2020

PubMed Abstract: 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.

PubMed: 32355044
DOI: 10.1107/S2059798320004398

Experimental method

X-RAY DIFFRACTION (2.957 Å)