Involved in the biosynthesis of polyacyltrehalose (PAT), a pentaacylated, trehalose-based glycolipid that could have a role in anchoring the bacterial capsule. Catalyzes the sequential transfer of two palmitoyl groups onto a single glucose residue of trehalose generating the diacylated product 2,3-diacyltrehalose (trehalose dipalmitate). Although palmitoyl-CoA (PCoA) seems to be the physiological acyl donor, PapA3 can also use docosanoyl (22-carbon saturated fatty acid) coenzyme A as acyl donor. a long-chain fatty acyl-CoA + alpha,alpha-trehalose = 2-O-(long-chain fatty acyl)-alpha,alpha-trehalose + CoA 2-O-(long-chain fatty acyl)-alpha,alpha-trehalose + a mycolipenoyl-CoA = 2-O-(long-chain fatty acyl)-3-O-mycolipenoyl-trehalose + CoA alpha,alpha-trehalose + hexadecanoyl-CoA = 2-O-hexadecanoyl-alpha,alpha-trehalose + CoA 2-O-hexadecanoyl-alpha,alpha-trehalose + hexadecanoyl-CoA = 2-O,3-O-dihexadecanoyl-alpha,alpha-trehalose + CoA Deletion of the gene prevents PAT synthesis. Belongs to the PapA acyltransferase family.