Table 1.

Identified Pol I phosphopeptides and –sites and corresponding amino acids in the Pol I homology model

Subunit	Phosphopeptide			3D-localization
	Position	Sequencea	Phosphosite	Amino acid in homology modelb
A190	352–366	ADSFFMDVLVVPPTR	S354	Rpb1 W234
	684–689	DSFFTR	S685	Rpb1 T539
	935–955	GSNVNVSQIMCLLGQQALEGR	S936 or S941c	Rpb1 S754/A759
A43	207–212	FSFGNR	S208	N/D
	213–228	SLGHWVDSNGEPIDGK	S220	A43 S220
	242–264	VVSVDGTLISDADEEGNGYNSSR	S262 or S263c	N/D
	278–289	IVFDDEVSIENK	S285	N/D
A34.5	7–31	DYVSDSDSDDEVISNEFSIPDGFKK	S10/S12/S14	N/D
ABC23	98–119	ALQISMNAPVFVDLEGETDPLR	S102	ABC23 S102
AC19	21–46	HIQEEEEQDVDMTGDEEQEEEPDREK	T33	Rpb11 A3
	49–77	LLTQATSEDGTSASFQIVEEDHTLGNALR	T51 or T54 or S55c	Rpb11 I21/D24/T25

^aPhosphoserines/-threonines are presented as bold, underlined characters.

^bSome phosphosites could not be localized in the Pol I homology model due to weak homology of the respective protein regions to Pol II, missing homologous subunits or deletions in the A43/14 crystal structure.

^cThree phosphopeptides could be identified due to the specific mass shift after chemical derivatization and a partial MS/MS spectrum, but the phosphorylation site could not be unambiguously assigned. The remaining possible serines and threonines are shown in bold, italic letters in the peptide sequence.