Mediates the incorporation of phosphate into starch-like phospho-alpha-glucan, mostly at the C-3 position of glucose units. Required for starch degradation, suggesting that the phosphate content of starch regulates its degradability. [(1->4)-6-phospho-alpha-D-glucosyl](n) + n ATP + n H2O = [(1->4)-3,6-bisphospho-alpha-D-glucosyl](n) + n AMP + 2n H(+) + n phosphate Homodimer. Starch granules during starch mobilization in darkness. A number of isoforms are produced. According to EST sequences. In all starch containing tissues (e.g. roots, leaves, stems, inflorescence and siliques). Circadian regulation. Induced during light phase and repressed during dark phase. The N-terminal domain contains the alpha-glucan binding site, the central domain the pyrophosphate/phosphate carrier histidine, and the C-terminal domain the ATP binding site. The reaction takes place in three steps, mediated by a phosphocarrier histidine residue located on the surface of the central domain. The two first partial reactions are catalyzed at an active site located on the C-terminal domain, and the third partial reaction is catalyzed at an active site located on the N-terminal domain. For catalytic turnover, the central domain swivels from the concave surface of the C-terminal domain to that of the N-terminal domain (By similarity). Belongs to the PEP-utilizing enzyme family.