Structure PAPS binding

The plant soluble STs have around 25 to 30% amino acid identity with mammalian soluble STs, and are of a similar size. Comparisons between F. chloraefolia F3ST and F4 ST, combined with mutational analysis and data from the crystal structure of mouse estrogen ST, have defined amino acid residues important for PAPS binding, substrate binding and catalysis, and the mechanism of sulfonate transfer. " Sequence relatedness has been used to divide the STs into families and subfamilies in a similar manner as for P450s. ... 

The active site similarities listed above belie a remarkable functional diversity, which includes phosphate ester hydrolysis, dioxygen and NO reduction, reversible O2 binding, and O2 activation, the last of which includes enzymes involved in ribonucleotide reduction, hydrocarbon monooxygenation, and fatty acyl desaturation. At the overall protein level, the purple acid phosphatases (PAPs) seem to be completely unrelated, both structurally and functionally, to any of the others in this class. Similarly, the flavo-diiron enzymes form a structurally and probably functionally distinct family of proteins, catalyzing both dioxygen and NO reduction. These last two examples illustrate that attempts to shoehorn all of these enzymes into a single class can sometimes provide a simplistic and misleading view of their chemistry and biochemistry. 

Proteins are constructed of modular systems or domains. These are portions of the polypeptide chain that can fold independendy into a stable structure. A protein may be just one domain, or may be comprised of many domains. A typical domain may be roughly 25 A in diameter and consist of 100-150 amino acid residues. For example, two a helices, joined by a loop (the helix-loop-helix motif) can give a calcium-binding motif or a DNA-binding motif. The so called Greek key motif consists of four antiparallel P strands arranged in a pattern reminiscent of one found in ancient Greekffiezes (80). The PaP motif consists of two P strands that are parallel but not necessarily adjacent connected by an a helix, which shields the strands from solvent. Some examples of these types of motifs are shown in Fig. 33. 

The best available example to understand how the sulfotransferases interact with their substa tes is from the study of the structure of a ternary complex of 3-OST-3/PAP/tetrasaccharide (where PAP represents 3 -phosphoadenosine 5 -phosphate). From this structure, one can clearly observe e interaction between the amino acid residues that participate in the binding to the substrate. The 3-OH position of the glucosamine unit (acceptor site) is locked into a position that is about 2.8 A to the catalytic base residue. At least sbc amino acid residues interact with the different functional groups of the saccharide units around the reducing end and the nonreducing end of the glucosamine acceptor (Figure 10). 

FIGURE 18.5 (a) a-Helix (1) or (2) (b) P-sheet (c) PaP (a super secondary structure) (d) a twin (e) a helix-loop-helix binding (/) a catalytic triad. 

Fig. 3.2 Numbers of atoms in the intracellular binding site of E. coli CLC Cl transporter by conventional QM/MM-LPS dashed, upper panel), PAP dotted, middle panel), and mPAP solid, lower panel) dynamics simulations, respectively. The binding site is defined to be a sphere of 6.0 A radius centered at the initial position of the Cl ion in the binding site at the beginning of the simulations. The model was built based on the crystal structure (PDB code lOTS) [80]. (Re-plotted with permission based on the data from [66], Copyright 2014 American Chemical Society.)...

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