HMA (heavy metal associated) is a member of the ATPases protein family involved in metal transport in plants. This study characterizes several HMA3 homologs and infers their molecular functions in different plant species. Arabidopsis AtHMA3 (AT4G30120) was used as a reference to retrieve 11 HMA3 homologs having 97–100% query cover, 535–542 residues, 56,983 to 58,642 (Da) molecular weight, and 5.74 to 8.16 pI value, 29.10 to 33.89 instability index, and 0.222 to 0.380 grand average of hydropathicity. Topological analyses showed 4 transmembrane domains in these HMA3 homologs positioned similarly in terms of cytoplasmic and non-cytoplasmic regions along with ∼22–28% α-helices, ∼22–28% extended strands, and ∼50% random coils. HMA3 protein of Arabidopsis lyrata subsp. lyrata and Eutrema salsugineum are located at chromosome 2, while others are positioned at chromosome 4. All these HMA3 homologs are localized in the plasma membrane sharing a few common biological and molecular functions. Besides, these HMA3 genes contain 8–9 exons in which promoter positions are varied among the homologs. The cis-acting elements of HMA3 genes were projected to be involved with stress response, anaerobic induction, and light-responsive regulation in plants. Three out of five motifs encode E1-E2_ATPase involved in proton-pumping in the plasma membrane. The Arabidopsis thaliana HMA3 protein clustered with Camelina sativa and Capsella rubella show a close phylogenetic relationship. Also, AtHMA3 exhibits a close association with AtHMA3 with MTPA2, ZAT, NRAMP3, IRT2, and NRAMP2 under the local network of AtHMA3 linked to metal transport. Further, AtHMA3 is most potentially expressed during senescence, germinating seed, seedlings, young rosette, bolting, and young flower. In addition, AtHMA3 showed a significant upregulation (>6.0 fold) under Fe-deficiency. These findings may provide essential background to perform wet-lab experiments to understand the role of HMA3 in metal homeostasis.
