Involved in the biosynthesis of L-colitose, a 3,6-dideoxyhexose present in the O-antigen region of lipopolysaccharides (LPS), where it serves as an antigenic determinant and is vital for bacterial defense and survival. Catalyzes the removal of the C3'-hydroxyl group from GDP-4-keto-6-deoxy-D-mannose via a combined transamination-deoxygenation reaction. The catalysis is initiated by a transamination step in which pyridoxal 5'-phosphate (PLP) is converted to pyridoxamine 5'-phosphate (PMP) in the presence of L-glutamate. This coenzyme then forms a Schiff base with GDP-4-keto-6-deoxy-D-mannose and the resulting adduct undergoes a PMP-mediated beta-dehydration reaction to give a sugar enamine intermediate, which after tautomerization and hydrolysis to release ammonia yields GDP-4-keto-3,6-dideoxy-D-mannose as a product. In vitro, is able to catalyze the formation of GDP-4-keto-3,6-dideoxymannose using GDP-perosamine rather than GDP-4-keto-6-deoxymannose as a substrate, with no need of glutamate. GDP-4-dehydro-alpha-D-rhamnose + L-glutamate = 2-oxoglutarate + GDP-4-dehydro-3,6-dideoxy-alpha-D-mannose + NH4(+) Nucleotide-sugar metabolism; GDP-L-colitose biosynthesis. Homodimer. Belongs to the DegT/DnrJ/EryC1 family.