TCDB is operated by the Saier Lab Bioinformatics Group

2.A.4 The Cation Diffusion Facilitator (CDF) Family

The CDF family is a ubiquitous family, members of which are found in bacteria, archaea and eukaryotes (Paulsen and Saier, 1997). They transport heavy metals including cobalt, cadmium, zinc and possibly nickel, copper and mercuric ions. There are 9 mammalian paralogues, ZnT1 - 8 and 10 (Cousins et al., 2006; Kambe 2012). Most members of the CDF family possess six putative transmembrane spanners with N- and C-termini on the cytoplasmic side of the membrane, but MSC2 of S. cerevisiae (TC #2.A.4.4.1) and Znt5 and hZTL1 (2.A.4.4.3) of H. sapiens exhibit 15 and 12 putative TMSs, respectively (Cragg et al., 2002). These proteins exhibit an unusual degree of sequence divergence and size variation (300-750 residues). Eukaryotic proteins exhibit differences in cell localization. Some catalyze heavy metal uptake from the cytoplasm into various intracellular eukaryotic organelles (ZnT2-7) while others (ZnT1) catalyze efflux from the cytoplasm across the plasma membrane into the extracellular medium. Thus, some are found in plasma membranes while others are in organellar membranes such as vacuoles of plants and yeast and the golgi of animals (Chao and Fu, 2004b; Haney et al., 2005; MacDiarmid et al., 2003).They catalyze cation:proton antiport, have a single essential zinc-binding site within the transmembrane domains of each monomer within the dimer, and have a binuclear zinc-sensing and binding site in the cytoplamsic C-terminal region (Kambe 2012).

Prokaryotic and eukaryotic proteins cluster separately but probably function with the same polarity by similar mechanisms. These proteins are secondary carriers which utilize the pmf and function by H antiport (for metal efflux). One member, CzcD of Bacillus subtilis, has been shown to exchange the divalent cation (Zn2+  or Cd2+ ) for two monovalent cations (K+ and H+ ) in an electroneutral process energized by the transmembrane pH gradient (Guffanti et al., 2002). Another, ZitB of E. coli (TC #2.A.4.1.4), has been reconstituted in proteoliposomes and studied kinetically (Chao and Fu, 2004a). It appears to function by simple Me2+ :H antiport with a 1:1 stoichiometry.

Montanini et al (2007) have conducted phylogenetic analysis of CDF family members. Their analysis revealed three major and two minor phylogenetic groups. They suggest that the three major groups segregated according to metal ion specificity: (1) Mn2+ , (2) Fe2+  and Zn2+  as well as other metal ions, and (3) Zn2+  plus other metals, but not Iron. CDF proteins have 6 TMSs with three 2 TMSs repeats. They are related to CRAC Ca2+  channels (TC#1.A.52) which has 4 TMSs (Matias et al., 2010).

At least two metal binding sites have been identified in the E. coli paralogue, YiiP (TC #2.A.4.1.5), and one plays a role in H+ binding as well (Chao and Fu, 2004b). The two Zn2+/Cd2+  binding sites consist of two interacting conserved aspartyl residues (Asp-157 and Asp-49), both in 2 fold symmetry-related TMS 5 and TMS 2, respectively, at the dimer interface of the homodimer (Wei and Fu, 2006). The (Asp-49 and Asp-157) may form a bimetal binding center. Two bound Cd2+  were transported cooperatively with sigmoidal dependency on the Cd2+  concentration. A translocation pathway for metal ions at the dimer interface has been proposed (Wei and Fu, 2006). CDF family members may generally be homodimeric (Haney et al., 2005; Wei et al., 2004).

Lu and Fu (2007) have reported the x-ray structure of YiiP of E. coli (2.A.4.7.1) in complex with zinc at 3.8 angstrom resolution. YiiP is a homodimer held together in a parallel orientation through four Zn2+  ions at the interface of the cytoplasmic domains.  The two transmembrane domains swing out to yield a Y-shaped structure. In each protomer, the cytoplasmic domain adopts a metallochaperone-like protein fold. The transmembrane domain features a bundle of six transmembrane helices and a tetrahedral Zn2+  binding site located in a cavity that is open to both the membrane outer leaflet and the periplasm. 

Coudray et al. (2013) used cryoelectron microscopy to determine a 13-Å resolution structure of a YiiP homolog from Shewanella oneidensis within a lipid bilayer in the absence of Zn2+. Starting from the X-ray structure in the presence of Zn2+, they used molecular dynamic flexible fitting to build a model. Comparison of the structures suggested a conformational change that involves pivoting of a transmembrane, four-helix bundle (M1, M2, M4, and M5) relative to the M3-M6 helix pair. Although accessibility of transport sites in the X-ray model indicates that it represents an outward-facing state, their model was consistent with an inward-facing state, suggesting that the conformational change is relevant to the alternating access mechanism for transport. They speculated that the dimer may coordinate rearrangement of the transmembrane helices,

Involved in metal tolerance/resistance by efflux, most CDF proteins share a two-modular architecture consisting of a transmembrane domain (TMD) and a C-terminal domain (CTD) that protrudes into the cytoplasm. A Zn2+ and Cd2+ CDF transporter from the marine bacterium, Maricaulis maris, that does not possess the CTD is a member of a new, CTD-lacking subfamily of CDFs.

The generalized transport reaction for CDF family members is:

Me2+  (in) H+ (out) ± K+ (out) → Me2+  (out) H+ (in) ± K+ (in).



References associated with 2.A.4 family:

Anton, A., A. Weltrowski, C.J. Haney, S. Franke, G. Grass, C. Rensing, and D.H. Nies. (2004). Characteristics of zinc transport by two bacterial cation diffusion facilitators from Ralstonia metallidurans CH34 and Escherichia coli. J. Bacteriol. 186: 7499-7507. 15516561
Burré, J., H. Zimmermann, and W. Volknandt. (2007). Identification and characterization of SV31, a novel synaptic vesicle membrane protein and potential transporter. J Neurochem 103: 276-287. 17623043
Chao, Y. and D. Fu. (2004a). Kinetic study of the antiport mechanism of an Escherichia coli zinc transporter, ZitB. J. Biol. Chem. 279: 12043-12050. 14715669
Chao, Y. and D. Fu. (2004b). Thermodynamic studies of the mechanism of metal binding to the Escherichia coli zinc transporter YiiP. J. Biol. Chem. 279: 17173-17180. 14960568
Chen, X., J. Li, L. Wang, G. Ma, and W. Zhang. (2016). A mutagenic study identifying critical residues for the structure and function of rice manganese transporter OsMTP8.1. Sci Rep 6: 32073. 27555514
Cherezov, V., N. Höfer, D.M. Szebenyi, O. Kolaj, J.G. Wall, R. Gillilan, V. Srinivasan, C.P. Jaroniec, and M. Caffrey. (2008). Insights into the mode of action of a putative zinc transporter CzrB in Thermus thermophilus. Structure 16: 1378-1388. 18786400
Clemens, S., T. Bloss, C. Vess, D. Neumann, D.H. Nies, and U. zur Nieden. (2002). A transporter in the endoplasmic reticulum of Schizosaccharomyces pombe cells mediates zinc storage and differentially affects transition metal tolerance. J. Biol. Chem. 277: 18215-18221. 11886869
Coudray, N., S. Valvo, M. Hu, R. Lasala, C. Kim, M. Vink, M. Zhou, D. Provasi, M. Filizola, J. Tao, J. Fang, P.A. Penczek, I. Ubarretxena-Belandia, and D.L. Stokes. (2013). Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy. Proc. Natl. Acad. Sci. USA 110: 2140-2145. 23341604
Cousins, R.J., J.P. Liuzzi, and L.A. Lichten. (2006). Mammalian zinc transport, trafficking, and signals. J. Biol. Chem. 281: 24085-24089. 16793761
Cragg, R.A., G.R. Christie, S.R. Phillips, R.M. Russi, S. Kury, J.C. Mathers, P.M. Taylor, and D. Ford. (2002). A novel zinc-regulated human zinc transporter, hZTL1, is localized to the enterocyte apical membrane. J. Biol. Chem. 277: 22789-22797. 11937503
Cuajungco MP., Basilio LC., Silva J., Hart T., Tringali J., Chen CC., Biel M. and Grimm C. (2014). Cellular zinc levels are modulated by TRPML1-TMEM163 interaction. Traffic. 15(11):1247-65. 25130899
Cuajungco, M.P. and K. Kiselyov. (2017). The mucolipin-1 (TRPML1) ion channel, transmembrane-163 (TMEM163) protein, and lysosomal zinc handling. Front Biosci (Landmark Ed) 22: 1330-1343. 28199205
Dechen, K., C.D. Richards, J.C. Lye, J.E. Hwang, and R. Burke. (2015). Compartmentalized zinc deficiency and toxicities caused by ZnT and Zip gene over expression result in specific phenotypes in Drosophila. Int J Biochem. Cell Biol. 60: 23-33. 25562517
Desbrosses-Fonrouge, A.G., K. Voigt, A. Schröder, S. Arrivault, S. Thomine, and U. Krämer. (2005). Arabidopsis thaliana MTP1 is a Zn transporter in the vacuolar membrane which mediates Zn detoxification and drives leaf Zn accumulation. FEBS Lett. 579: 4165-4174. 16038907
Ellis, C.D., C.W. Macdiarmid, and D.J. Eide. (2005). Heteromeric protein complexes mediate zinc transport into the secretory pathway of eukaryotic cells. J. Biol. Chem. 280: 28811-28818. 15961382
Fujiwara T., Kawachi M., Sato Y., Mori H., Kutsuna N., Hasezawa S. and Maeshima M. (2015). A high molecular mass zinc transporter MTP12 forms a functional heteromeric complex with MTP5 in the Golgi in Arabidopsis thaliana. FEBS J. 282(10):1965-79. 25732056
Fukunaka, A., T. Suzuki, Y. Kurokawa, T. Yamazaki, N. Fujiwara, K. Ishihara, H. Migaki, K. Okumura, S. Masuda, Y. Yamaguchi-Iwai, M. Nagao, and T. Kambe. (2009). Demonstration and characterization of the heterodimerization of ZnT5 and ZnT6 in the early secretory pathway. J. Biol. Chem. 284: 30798-30806. 19759014
Grass, G., M. Otto, B. Fricke, C.J. Haney, C. Rensing, D.H. Nies, and D. Munkelt. (2005). FieF (YiiP) from Escherichia coli mediates decreased cellular accumulation of iron and relieves iron stress. Arch. Microbiol. 183: 9-18. 15549269
Grover, A. and R. Sharma. (2006). Identification and characterization of a major Zn(II) resistance determinant of Mycobacterium smegmatis. J. Bacteriol. 188: 7026-7032. 16980506
Guffanti, A.A., Y. Wei, S.V. Rood, and T.A. Krulwich. (2002). An antiport mechanism for a member of the cation diffusion facilitator family: divalent cations efflux in exchange for K+ and H+. Mol. Microbiol. 45: 145-153. 12100555
Gupta, S., J. Chai, J. Cheng, R. D'Mello, M.R. Chance, and D. Fu. (2014). Visualizing the kinetic power stroke that drives proton-coupled zinc(II) transport. Nature 512: 101-104. 25043033
Haney, C.J., G. Grass, S. Franke, and C. Rensing. (2005). New developments in the understanding of the cation diffusion facilitator family. J. Ind. Microbiol. Biotechnol. 32: 215-226. 15889311
Hložková, K., J. Suman, H. Strnad, T. Ruml, V. Paces, and P. Kotrba. (2013). Characterization of pbt genes conferring increased Pb2+ and Cd2+ tolerance upon Achromobacter xylosoxidans A8. Res. Microbiol. 164: 1009-1018. 24125695
Höfer, N., O. Kolaj, H. Li, V. Cherezov, R. Gillilan, J.G. Wall, and M. Caffrey. (2007). Crystallization and preliminary X-ray diffraction analysis of a soluble domain of the putative zinc transporter CzrB from Thermus thermophilus. Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 673-677. 17671365
Huang L., Gitschier J. (1997). A novel gene involved in zinc transport is deficient in the lethal milk mouse. Nat. Genet. 17: 292-297. 9354792
Ishihara, K., T. Yamazaki, Y. Ishida, T. Suzuki, K. Oda, M. Nagao, Y. Yamaguchi-Iwai, and T. Kambe. (2006). Zinc transport complexes contribute to the homeostatic maintenance of secretory pathway function in vertebrate cells. J. Biol. Chem. 281: 17743-17750. 16636052
Jakubovics, N.S. and R.A. Valentine. (2009). A new direction for manganese homeostasis in bacteria: identification of a novel efflux system in Streptococcus pneumoniae. Mol. Microbiol. 72: 1-4. 19226325
Kambe, T. (2012). Molecular architecture and function of ZnT transporters. Curr Top Membr 69: 199-220. 23046652
Kambe, T., H. Narita, Y. Yumaguchi-Iwa, J. Hirose, T. Amano, N. Sugiura, R. Sasaki, K. Mori. T. Iwanaga, and M. Nagano. Cloning and characterization of a novel mammalian J. Biol. Chem. 277: 19049-1955. 11904301
Kawachi M., Kobae Y., Kogawa S., Mimura T., Kramer U. and Maeshima M. (2012). Amino acid screening based on structural modeling identifies critical residues for the function, ion selectivity and structure of Arabidopsis MTP1. FEBS J. 279(13):2339-56. 22520078
Kawachi, M., Y. Kobae, T. Mimura, and M. Maeshima. (2008). Deletion of a histidine-rich loop of AtMTP1, a vacuolar Zn2+/H+ antiporter of Arabidopsis thaliana, stimulates the transport activity. J. Biol. Chem. 283: 8374-8383. 18203721
Kolaj-Robin, O., D. Russell, K.A. Hayes, J.T. Pembroke, and T. Soulimane. (2015). Cation Diffusion Facilitator family: Structure and function. FEBS Lett. 589: 1283-1295. 25896018
Lee, S.M., G. Grass, C.J. Haney, B. Fan, B.P. Rosen, A. Anton, D.H. Nies, and C. Rensing. (2002). Functional analysis of the Escherichia coli zinc transporter ZitB. FEMS Microbiol. Lett. 215: 273-278. 12399046
Li, L. and J. Kaplan. (2001). The yeast gene MSC2, a member of the cation diffusion facilitator family, affects the cellular distribution of zinc. J. Biol. Chem. 276: 5036-5043. 11058603
Lin H., Burton D., Li L., Warner DE., Phillips JD., Ward DM. and Kaplan J. (2009). Gain-of-function mutations identify amino acids within transmembrane domains of the yeast vacuolar transporter Zrc1 that determine metal specificity. Biochem J. 422(2):273-83. 19538181
Lin, H., A. Kumánovics, J.M. Nelson, D.E. Warner, D.M. Ward, and J. Kaplan. (2008). A single amino acid change in the yeast vacuolar metal transporters ZRC1 and COT1 alters their substrate specificity. J. Biol. Chem. 283: 33865-33873. 18930916
Lisher, J.P., K.A. Higgins, M.J. Maroney, and D.P. Giedroc. (2013). Physical characterization of the manganese-sensing pneumococcal surface antigen repressor from Streptococcus pneumoniae. Biochemistry 52: 7689-7701. 24067066
Lopez, V. and S.L. Kelleher. (2009). Zinc transporter-2 (ZnT2) variants are localized to distinct subcellular compartments and functionally transport zinc. Biochem. J. 422: 43-52. 19496757
Lu, M. and D. Fu. (2007). Structure of the zinc transporter YiiP. Science 317: 1746-1748. 17717154
Lye, J.C., C.D. Richards, K. Dechen, C.G. Warr, and R. Burke. (2013). In vivo zinc toxicity phenotypes provide a sensitized background that suggests zinc transport activities for most of the Drosophila Zip and ZnT genes. J Biol Inorg Chem 18: 323-332. 23322169
MacDiarmid, C.W., M.A. Milanick, and D.J. Eide. (2003). Induction of the ZRC1 metal tolerance gene in zinc-limited yeast confers resistance to zinc shock. J. Biol. Chem. 278: 15065-15072. 12556516
Martin, J.E. and D.P. Giedroc. (2016). Functional determinants of metal ion transport and selectivity in paralogous cation diffusion facilitator transporters CzcD and MntE in Streptococcus pneumoniae. J. Bacteriol. [Epub: Ahead of Print] 26787764
Matias, M.G., K.M. Gomolplitinant, D.G. Tamang, and M.H. Saier, Jr. (2010). Animal Ca2+ release-activated Ca2+ (CRAC) channels appear to be homologous to and derived from the ubiquitous cation diffusion facilitators. BMC Res Notes 3: 158. 20525303
Migocka, M., A. Kosieradzka, A. Papierniak, E. Maciaszczyk-Dziubinska, E. Posyniak, A. Garbiec, and S. Filleur. (2015). Two metal-tolerance proteins, MTP1 and MTP4, are involved in Zn homeostasis and Cd sequestration in cucumber cells. J Exp Bot 66: 1001-1015. 25422498
Mitchell, R.K., M. Hu, P.L. Chabosseau, M.C. Cane, G. Meur, E.A. Bellomo, R. Carzaniga, L.M. Collinson, W.H. Li, D.J. Hodson, and G.A. Rutter. (2016). Molecular Genetic Regulation of Slc30a8/ZnT8 Reveals a Positive Association With Glucose Tolerance. Mol Endocrinol 30: 77-91. 26584158
Montanini B., D. Blaudez, S. Jeandroz, D. Sanders, M. Chalot. (2007). Phylogenetic and functional analysis of the Cation Diffusion Facilitator (CDF) family: improved signature and prediction of substrate specificity. BMC Genomics. 8: 107. 17448255
Munkelt, D., G. Grass, and D.H. Nies. (2004). The chromosomally encoded cation diffusion facilitator proteins DmeF and FieF from Wautersia metallidurans CH34 are transporters of broad metal specificity. J. Bacteriol. 186: 8036-8043. 15547276
Nies, D.H. and S. Silver. (1995). Ion efflux systems involved in bacterial metal resistances. J. Industr. Microbiol. 14: 186-199. 7766211
Nishito, Y., N. Tsuji, H. Fujishiro, T.A. Takeda, T. Yamazaki, F. Teranishi, F. Okazaki, A. Matsunaga, K. Tuschl, R. Rao, S. Kono, H. Miyajima, H. Narita, S. Himeno, and T. Kambe. (2016). Direct Comparison of Manganese Detoxification/Efflux Proteins and Molecular Characterization of ZnT10 as a Manganese Transporter. J. Biol. Chem. [Epub: Ahead of Print] 27226609
Paulsen, I.T. and M.H. Saier, Jr. (1997). A novel family of ubiquitous heavy metal ion transport proteins. J. Membr. Biol. 156: 99-103. 9075641
Peiter E., B. Montanini, A. Gobert, P. Pedas, S. Husted, F.J. Maathuis, D. Blaudez, M. Chalot, D. Sanders. (2007). A secretory pathway-localized cation diffusion facilitator confers plant manganese tolerance. Proc. Natl. Acad. Sci. U.S.A. 104: 8532-8537. 17494768
Podar, D., J. Scherer, Z. Noordally, P. Herzyk, D. Nies, and D. Sanders. (2012). Metal selectivity determinants in a family of transition metal transporters. J. Biol. Chem. 287: 3185-3196. 22139846
Rahman, M., S.G. Patching, F. Ismat, P.J. Henderson, R.B. Herbert, S.A. Baldwin, and M.J. McPherson. (2008). Probing metal ion substrate-binding to the E. coli ZitB exporter in native membranes by solid state NMR. Mol. Membr. Biol. 25: 683-690. 19039702
Raimunda, D. and G. Elso-Berberián. (2014). Functional characterization of the CDF transporter SMc02724 (SmYiiP) in Sinorhizobium meliloti: Roles in manganese homeostasis and nodulation. Biochim. Biophys. Acta. 1838: 3203-3211. 25242380
Rosch, J.W., G. Gao, G. Ridout, Y.D. Wang, and E.I. Tuomanen. (2009). Role of the manganese efflux system mntE for signalling and pathogenesis in Streptococcus pneumoniae. Mol. Microbiol. 72: 12-25. 19226324
Sácký, J., T. Leonhardt, and P. Kotrba. (2016). Functional analysis of two genes coding for distinct cation diffusion facilitators of the ectomycorrhizal Zn-accumulating fungus Russula atropurpurea. Biometals 29: 349-363. 26906559
Sindreu, C., R.D. Palmiter, and D.R. Storm. (2011). Zinc transporter ZnT-3 regulates presynaptic Erk1/2 signaling and hippocampus-dependent memory. Proc. Natl. Acad. Sci. USA 108: 3366-3370. 21245308
Tanaka, N., M. Kawachi, T. Fujiwara, and M. Maeshima. (2013). Zinc-binding and structural properties of the histidine-rich loop of Arabidopsis thaliana vacuolar membrane zinc transporter MTP1. FEBS Open Bio 3: 218-224. 23772397
Uebe, R., K. Junge, V. Henn, G. Poxleitner, E. Katzmann, J.M. Plitzko, R. Zarivach, T. Kasama, G. Wanner, M. Pósfai, L. Böttger, B. Matzanke, and D. Schüler. (2011). The cation diffusion facilitator proteins MamB and MamM of Magnetospirillum gryphiswaldense have distinct and complex functions, and are involved in magnetite biomineralization and magnetosome membrane assembly. Mol. Microbiol. 82: 818-835. 22007638
Valentine, R. A., K. A. Jackson, G. R. Christie, J. C. Mathers, P. M. Taylor, and D. Ford. (2007). ZnT5 Variant B Is a Bidirectional Zinc Transporter and Mediates Zinc Uptake in Human Intestinal Caco-2 Cells. J. Biol. Chem. 282: 14389-14393 17355957
Wei, Y. and D. Fu. (2006). Binding and transport of metal ions at the dimer interface of the Escherichia coli metal transporter YiiP. J. Biol. Chem. 281: 23492-23502. 16790427
Wei, Y., L. Huilin, and F. Dax. (2004). Oligomeric state of the Escherichia coli metal transporter YiiP. J. Biol. Chem. 279: 39251-39259. 15258151
Weijers, R.N. (2010). Three-dimensional structure of β-cell-specific zinc transporter, ZnT-8, predicted from the type 2 diabetes-associated gene variant SLC30A8 R325W. Diabetol Metab Syndr 2: 33. 20525392
Xiong, A. and R.K. Jayaswal. (1998). Molecular characterization of a chromosomal determinant conferring resistance to zinc and cobalt ions in Staphylococcus aureus. J. Bacteriol. 180: 4024-4029. 9696746
Zogzas, C.E., M. Aschner, and S. Mukhopadhyay. (2016). Structural elements in the transmembrane and cytoplasmic domains of the metal transporter SLC30A10 are required for its manganese efflux activity. J. Biol. Chem. [Epub: Ahead of Print] 27307044