. 2014 Dec 23;10(3):652–666. doi: 10.1021/cb500860x

Table 1. Summary of Structural and Biochemical Data on Phosphorylated RNA Binding Proteins.

RNA-binding protein (PDB codes available)	structure determination method	phosphorylated site/s	mechanism	kinase	change in K_d toward RNA due to phosphorylation	change in K_d toward protein target due to phosphorylation
SFRS1	NMR (1), MD (1), X-ray (2)	∼8–10 serines in RS1 by SRPK1; 20 serines by both SRPK1 and Clk	localized disorder to partial order transition upon phosphorylation	SRPK1 Clk/Sty	5–10 fold decrease in Ron ESE mRNA affinity due to hyperphosphorylation at 20 sites by EMSA and filter binding⁴⁰	not determined quantitatively
(1) RS1 domain only (no PDB code available)						not determined quantitatively
(1) RS1 domain only (no PDB code available)						interaction of SFRS1 with Transportin 3 is salt dependent with significant reduction in binding in 500 mM NaCl in GST pull-down experiments consistent with an electrostatic interaction³²
(2) RRM2-RS domain (3BEG bound to SRPK1; 4C0O bound to Transportin 3)
			localized disorder to order transition upon SRPK1 and Transportin 3 binding
SF1	X-ray and NMR	Ser80, Ser82	localized disorder to order transition upon phosphorylation	KIS kinase	not quantified; small increase in efficiency of RNA binding by SAXS and EMSA.^43,44	Small increase (<2-fold) in association by ITC⁴³
2M09 (free HH- NMR)
2M0G (unphosphorylated SF1 NYD bound to U2AF UHM – NMR)
2M0G (unphosphorylated SF1 NYD bound to U2AF UHM – NMR)						K_d values: pSF1 + U2AF65^RRM123 = 96 ± 32 nM; SF1 + U2AF65^RRM123 = 114 ± 23 nM
4FXW
(phosphorylated SF1 NTD bound to the U2AF UHM – X-ray) 4FXX (unphosphorylated SF1 NTD (residues 26–132))
SLBPL-motif	X-ray	Thr171(hSLBP)/ Thr230 (dSLBP)	localized disorder to order transition upon phosphorylation	unknown	7–11 fold increase in affinity toward histone mRNA stem-loop^75,76	>32-fold toward Pin1 using fluorescence anisotropy⁸⁰
			localized disorder to order transition upon phosphorylation	unknown possibly CK2
			unknown		∼27 fold increase in affinity toward histone mRNA stem-loop by dSLBP⁷⁵
4QOZ (T171 phos) 4L8R (T171 nonphos)
		Ser221, Ser222, and Thr226 (hSLBP)
		Ser269, Ser271, Ser273, Ser275 (dSLBP)
KSRP KH1	NMR, X-ray	Ser193	order to disorder, i.e., global unfolding of KH1 domain	AKT	no detectable difference by EMSA and ITC⁸⁹	>1000-fold increase in affinity toward 14–3–3ζ upon phosphorylation by ITC⁸⁹
2OPU (nonphos KH domain) 1QJB (phospho-Ser peptide bound to 14–3–3ζ)	NMR, X-ray	Ser193	order to disorder, i.e., global unfolding of KH1 domain	AKT	no detectable difference by EMSA and ITC⁸⁹
Upf1/SMG proteins	X-ray	Thr28, Ser1078, Ser1096, and Ser1116 in SQ motifs in Upf1	localized disorder to order transition upon phosphorylation	SMG-1; possibly other SQ kinases such as ATR, ATM, DNA-PK	unknown	>100-fold increase in affinity toward SMG7 upon phosphorylation by ITC¹⁰⁵ Binding to SMG5–SMG7, SMG6, and SMG7 is phosphorylation dependent in GST-pull down and coimmunoprecipitation experiments^103,104
1YA0 (N-terminal domain of SMG7)
4UM2 (TPR domain of SMG6)
3ZHE (C. elegans SMG5–SMG7)
TiaS	X-ray	Thr18	silent phosphorylation	unknown	no significant difference toward tRNA is predicted^111,112	N/A
(phosphorylated)
3AMT 3AMU 3AU7
Ire1	X-ray	Ser724 in activation segment (in human Ire1)	global conformational change involving dimerization and domain reorientation	Ire1 autophosphorylation	3–5 fold decrease in K_m for the RNA substrate due to phosphorylation at 1–4 sites; 2–40 fold effect on K_cat/K_m¹¹⁸	N/A
3P23 2RIO/3LJ0 3FBV	X-ray	Ser724 in activation segment (in human Ire1)		Ire1 autophosphorylation		N/A