Mediates the incorporation of phosphate into starch-like phospho-alpha-glucan, mostly at the C-3 position of glucose units. May be required for starch degradation, suggesting that the phosphate content of starch regulates its degradability (By similarity). [(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. 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.