Polyketide synthase involved in the biosynthesis of methyl-branched fatty acids such as mycolipanoic, mycolipenic (phthienoic) and mycolipodienoic acids required for the synthesis of a major class of polyacylated trehaloses. Catalyzes the elongation of CoA esters of long-chain fatty acids by incorporation of three methylmalonyl (but not malonyl) residues, to form trimethyl-branched fatty-acids. 3 (S)-methylmalonyl-CoA + a long-chain fatty acyl-CoA + 9 H(+) + holo-[mycolipanoate synthase] + 6 NADPH = 3 CO2 + 4 CoA + 3 H2O + long-chain mycolipanoyl-[mycolipanoate synthase] + 6 NADP(+) Lipid metabolism; fatty acid biosynthesis. Homodimer. Cells lacking this gene do not produce mycolipanoic acids, mycolipenic (phthienoic) or mycolipodienoic acids, the major constituents of polyacyltrehaloses, but synthesize all of the other classes of lipids. The absence of the major acyl chains that anchor the surface-exposed acyltrehaloses causes a novel growth morphology. The previously assigned stop codon (TAA) of pks3 (Rv1180) is found to be a Tyr codon (TAC), and with this change, pks3 and pks4 become a single open reading frame designated msl3 (PubMed:12207710). Large scale proteomics studies identify protein sequence that extends N-terminal to the initially annotated start site of Rv1181, more evidence that a single protein is translated from this locus. Rv1180 and Rv1181 have been merged into one gene. Rv1180 and Rv1181 have been merged into one gene.