Participates in the conversion of CDP-6-deoxy-D-glycero-L-threo-4-hexulose to 3,6-dideoxy-D-glycero-D-glycero-4-hexulose together with CDP-6-deoxy-D-glycero-L-threo-4-hexulose-3-dehydrase (E1) in two consecutive steps. The detailed mechanism of E3 is not yet resolved. Nucleotide-sugar biosynthesis; CDP-ascarylose biosynthesis. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Monomer.