Phenol sulfotransferase (PST) catalyzes sulfuryl group transfer from adenosine 3'-phosphate 5'-phosphosulfate (PAPS) to a variety of nucleophilic acceptors in biological system (reaction one). Physiological sulfation by PAPS results in the production of adenosine 3',5'-diphosphate (PAP). PAP may become a strong inhibitor or cofactor for the physiological or the transfer reactions, respectively. Several nucleotides other than PAP also serve as substrate, inhibitor or cofactor of PST catalyzed reaction (reaction two). We are interested in the effects of these nucleotides on the PST catalyzed reactions and their possible physiological significance of in biology. Several nucleotide inhibitors (such as adenosine 5'-diphosphate and adenosine 5'-triphosphate) of sulfotransferase in physiological reaction have been reported in the literature. However, our data suggests that they are not inhibitors for the transfer reaction or the reverse physiological reaction catalyzed by PST. The aim of this work is to show that the molecular docking analysis can be successfully used to underline the inhibition mechanism of these nucleotides.

Figure 1. The best docked conformations of nucleotides with 1aqu.

We docked all of the tested nucleotides, including PAP, PAPS, AMP, ADP, and ATP, into the active sites of both the complex of estrogen sulfotransferase with PAP(PDB entry: 1aqu) and the complex of estrogen sulfotransferase with PAPS (PDB entry: 1hy3). Figures 1 and Table 1 show the best docked results. The reference molecules are PAP and PAPS for 1aqu and 1hy3, respectively, when we calculated the RMSD values for all tested nucleotides (PAP, PAPS, AMP, ADP, and ATP). According to the RMSD values obtained, these docked structures for both sulfotransferases can be roughly divided into two categories. Table 1 shows the RMSD values of PAP, PAPS, AMP, ADP, and ATP that are less than 2.0 angstroms for the sulfotransferase 1aqu and 1hy3. The other category of RMSD values that are much more than 2.0 angstroms are not given.

Table 1. The results of nucleotide docking on 1aqu and 1hy3 with GEMDOCK
Minimization Energy of docked structure (cal/mole)
-192.12 -219.96 -151.03 -154.32 -193.83
RMSDa (angstroms) 0.51 1.06 1.25 0.76 1.85
Minimization Energy of docked structure (cal/mole)
-192.32 -222.97 -149.72 -173.03 -194.60
RMSDb (angstroms) 1.20 0.41 1.28 1.44 1.96
aThe values was calculated using reference molecule PAP for these tested nucleotides.
bThe values was calculated using reference molecule PAPS for these tested nucleotides.

Several nucleotides (such as PAP, AMP, ADP and ATP) of PST in physiological reaction showed to inhibit competitively the sulfation of PST when PAPS is the varied substrate (Table 2). Previous studies showed that various nucleotides bind tightly to PST (Table 3) and some nucleotides, 2',5'-PAP, AMP, 2':3'-cyclic PAP can be used by PST to replace PAP. Our experimental data suggests that these nucleotides are not inhibitors of the transfer reaction or the reverse physiological reaction catalyzed by PST (data not shown). To explain the above experimental data, we report our results on the docking of nucleotides to EST. These observations are in good agreement with the experimental data reported here. The docking results explain why all the nucleotides tested bind tightly to PST. It also explains why some nucleotides may replace PAP as substrates for PST.

Table 2. Inhibition constants for the competitive inhibition of sulfotransferase by Nucleotidesa
Inhibitors Ki (mM)
PAP 0.1 (0.01)b
AMP >1000
ADP 30.0 (1.2)
ATP 23.2 (0.7)
a Data obtained from Rens-Domiano, S. S.; Roth, J. A. J Neurochem. 1987, 48, 1411-1415
b Deviation between +0.01 and -0.01

Table 3. Nucleotides used for the docking in PST
Name Dissociation constants Abbrevation
Kd1 (nM) Kd2 (microM)
3'-phosphoadenosine 5'-phosphate 31 (4)a, b
20 c
152 (1)b
200 c
3'-phosphoadenosine 5'-phosphousulfate >>c >>c PAPS
Adenosine 5'-monophosphate 9.2 (0.3) 164 (4) AMP
Adenosine 5'-diphosphate 38 (1) 75.0 (0.3) ADP
Adenosine 5'-triphosphate 79 (1) 122 (1) ATP
a Deviation between +4 and -4
b Data obtained from Lin, E. S.; Yang, Y. S. Biochem Biophys Res Commun. 2000, 271, 818-822
c Data was too large to be measured. (Yang, Y. S.; Marshall, A. D.; McPhie, P.; Guo, W. X.; Xie, X.; Chen, X.; Jakoby, W. B. Protein Expression and Purification 1996, 8, 423-429)

Through the use of RMSD values, one can predict to which enzyme a specific substrate/inhibitor will best bind. In this study, it was known from experimental data that PAP binds better than other nucleotide to sulfotransferase.

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