In higher multicellular eukaryotes, highly specialized membrane structures or membrane trafficking events are required for supporting various physiological functions. SNAREs (soluble NSF attachment protein receptors) play an important role in specific membrane fusions. These protein receptors are assigned to subgroubs (Qa-, Qb-, Qc-, and R-SNARE) according to their specific SNARE structural motif. A specific set of Qa-, Qb-, and Qc-SNAREs, located on the target membrane, interact with R-SNARE on the vesicle to form a tight complex, leading to membrane fusion. The zig-1 mutant of Arabidopsis lacking Qb-SNARE VTI11 shows little shoot gravitropism and abnormal stem morphology. VTI11 and its homolog VTI12 exhibit partially overlapping but distinct intracellular localization and have different biological functions in plants. Little is known about how SNAREs are targeted to specific organelles, even though their functions and specific localization are closely linked. Here, we report that a novel mutation in VTI12 (zip1) was found as a dominant suppressor of zig-1. The zip1 mutation gave VTI12 the ability to function as VTI11 by changing both the specificity of SNARE complex formation and its intracellular localization. One amino acid substitution drastically altered VTI12, allowing it to suppress abnormalities of higher order physiological functions such as gravitropism and morphology. The zip1 mutation may be an indication of the flexibility in plant cell function afforded by gene duplication, particularly among the VTI11 genes and their recently diverged orthologs.