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TitleStructural basis of ion - substrate coupling in the Na-dependent dicarboxylate transporter VcINDY.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 2644, Year 2022
Publish dateMay 12, 2022
AuthorsDavid B Sauer / Jennifer J Marden / Joseph C Sudar / Jinmei Song / Christopher Mulligan / Da-Neng Wang /
PubMed AbstractThe Na-dependent dicarboxylate transporter from Vibrio cholerae (VcINDY) is a prototype for the divalent anion sodium symporter (DASS) family. While the utilization of an electrochemical Na gradient ...The Na-dependent dicarboxylate transporter from Vibrio cholerae (VcINDY) is a prototype for the divalent anion sodium symporter (DASS) family. While the utilization of an electrochemical Na gradient to power substrate transport is well established for VcINDY, the structural basis of this coupling between sodium and substrate binding is not currently understood. Here, using a combination of cryo-EM structure determination, succinate binding and site-directed cysteine alkylation assays, we demonstrate that the VcINDY protein couples sodium- and substrate-binding via a previously unseen cooperative mechanism by conformational selection. In the absence of sodium, substrate binding is abolished, with the succinate binding regions exhibiting increased flexibility, including HPb, TM10b and the substrate clamshell motifs. Upon sodium binding, these regions become structurally ordered and create a proper binding site for the substrate. Taken together, these results provide strong evidence that VcINDY's conformational selection mechanism is a result of the sodium-dependent formation of the substrate binding site.
External linksNat Commun / PubMed:35551191 / PubMed Central
MethodsEM (single particle)
Resolution2.83 - 3.23 Å
Structure data

25756

7t9f

EMDB-25756, PDB-7t9f:
Structure of VcINDY-apo
Method: EM (single particle) / Resolution: 3.23 Å

25757

7t9g

EMDB-25757, PDB-7t9g:
Structure of VcINDY-Na+
Method: EM (single particle) / Resolution: 2.83 Å

Chemicals

ChemComp-NA:
Unknown entry

ChemComp-HOH:
WATER

Source
  • vibrio cholerae (bacteria)
KeywordsMEMBRANE PROTEIN / TRANSPORTER

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