Mediates the isomerization of dTDP-6-deoxy-D-xylohex-4-ulose into dTDP-6-deoxy-D-xylohex-3-ulose in the biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-galactose, a glycan chain of the S-layer. dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-3-dehydro-6-deoxy-alpha-D-galactose Homodimer.