Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4

Sagar Antala; Sergey Ovchinnikov; Hetunandan Kamisetty; David Baker; Robert E. Dempski

doi:10.1074/jbc.M114.617613

Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4*

From the ^‡Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609 and
the ^§Howard Hughes Medical Institute,
^¶Department of Biochemistry, and
^‖Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195

↵2 To whom correspondence should be addressed: Dept. of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Rd., Worcester, MA 01609. Tel.: 508-831-4193; E-mail: rdempski{at}wpi.edu.

↵1 Both authors contributed equally to this work.

Background: ZIP transporters increase the cytosolic concentration of first row transition metals.

Results: We have developed a structural model of hZIP4 by combining protein prediction methods with in situ experiments.

Conclusion: Analysis of our experiments provides insight into the permeation pathway of hZIP4.

Significance: Comparison of this model to membrane transporter crystal structures provides a structural linkage to MFS proteins.

Abstract

Members of the Zrt and Irt protein (ZIP) family are a central participant in transition metal homeostasis as they function to increase the cytosolic concentration of zinc and/or iron. However, the lack of a crystal structure hinders elucidation of the molecular mechanism of ZIP proteins. Here, we employed GREMLIN, a co-evolution-based contact prediction approach in conjunction with the Rosetta structure prediction program to construct a structural model of the human (h) ZIP4 transporter. The predicted contact data are best fit by modeling hZIP4 as a dimer. Mutagenesis of residues that comprise a central putative hZIP4 transmembrane transition metal coordination site in the structural model alter the kinetics and specificity of hZIP4. Comparison of the hZIP4 dimer model to all known membrane protein structures identifies the 12-transmembrane monomeric Piriformospora indica phosphate transporter (PiPT), a member of the major facilitator superfamily (MFS), as a likely structural homolog.

Footnotes

↵* The research described within this manuscript was supported by the Worcester Polytechnic Institute Research Foundation and National Institutes of Health Grants GM105964 (to R. E. D.) and GM092802 (to D. B.). The authors declare that they have no conflicts of interest with the contents of this article.
↵ This article contains supplemental file hzip4_model_v1.pdb.