3D Structure of Phenylalanine Hydroxylase (PAH)

residues 118-424

CPK Color Scheme
C O N Fe S

Phenylalanine Hydroxylase (PAH) is a protein in the body which converts phenylalanine into tyrosine. (See my PAH gene/protein page here) This chime model displays the structure of the catalytic region of PAH (residues 118-424) crystallized with its cofactor tetrahydrobiopterin and a 3-(2-thienyl)-L-alanine, a substrate analog which mimics the structure of phenylalanine, but has different reactivity. The missing residues 425-452 make up the tetramerization domain, as is discussed below. This particular crystal was chosen since, as it contained a substrate analog and the cofactor needed for its activity and contained an iron ion in its catalytically active +2 oxidation state, it gave the most information about the active site of the enzyme.

The buttons below highlight features of interest from the protein structure:

To reset the protein to the original view at any time, click here.

To see the basic shape of the backbone protein, colored by group, click here. The protein is colored blue on the amino end and gradually becomes orange on the carboxyl end. The tetramerization domain which was not included on this crystal would extend as an alpha-helix from the orange carboxyl end to the left in this view, approximately 25 residues (residues 425-452). The full-sized protein exists in an equilibrium between dimer and tetramer structures, with interactions between proteins localized to the tetramerization domain.

To see the ribbon structure of the protein, showing the secondary structure, with the cofactor, substrate analog, and iron (II) ion shown in space-filling display with CPK colors, click here.

To see a close up of the spatial relationship between the substrate analog (on right), the reduced tetrahydrobiopterin (on left), and the catalytically active iron (II) iron, click here. If the actual substrate were in the active site, the tetrahydrobiopterin would be oxidized to dihydrobiopterin during reaction.

To see pi-stacking intereactions between the cofactor and substrate analog (in CPK colors) and protein residues (phe 254 with the cofactor on the left and his 285 with the substrate analog on the right) in purple, click here. The pi-stacking interaction assists in holding the substrate (analog) and cofactor in position. To get a better view of the interaction, first select the four cyclic residues: right click, mouse to Select, mouse to Mouse Click Action, and click on Toggle Residue's Selected State. Then click on each of the four cyclic residues (they should turn orange). Now, right click, mouse to Options, then Dot surface, then click Van der Walls Radii. Now deselect the cyclic residues by clicking, or turn off highlighting of selected items.

To see the 5-coordinate ligands of the iron (II) ion, click here. (It may be helpful to slide the view down using Control+right mouse button.) On the left is a water molecule coordinated to the iron and crystallized with the protein. The residues, clockwise from the water molecule are glu 330, his 290, and his 285, which coordinate the iron via oxygen, nitrogen, and nitrogen atoms, respectively. These are some of the interactions which hold the iron (II) ion in the enzyme, which is crucial for its activity.

When the substrate analog binds to the enzyme, the enzyme goes through a substantial change in structure, the most notable part of which is the hinge-like action of the loop highlighted here. The residue shaded lighter orange than the rest is tyrosine 138, which moves 9.6 angstroms, more than any other residue during the conformational change. When the substrate analog binds, the enzyme closes up and become more compact, with the gate-like tyr 138 trapping the substrate analog and presumably initiating reaction when the actual substrate binds.


Andersen OA, Flatmark T, Hough E. 2002. Crystal Structure of the Ternary Complex of the Catalytic Domain of Human Phenylalanine Hydroxylase with Tetrahydrobiopterin and 3-(2-Thienyl)-L-alanine, and its Implications for the Mechanism of Catalysis and Substrate Activation. J. Mol. Biol. 320:1095-1108.

Protein structural data from file 1KW0.pdb obtained from the protein data bank and deposited with the above paper.

*This page was created as an assignment for an undergraduate molecular biology course. Please address questions or comments to: ismiller@davidson.edu

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