Phenylketonuria (PKU) – Structure of Phenylalanine

Hydroxylase Biol 405 –Molecular Medicine

1998 – Crystal structure of phenylalanine hydroxylase solved. The polypeptide consists of three regions: Regulatory domain (1-142) - a 4 stranded anti-parallel -sheet flanked on one side by 2 short -helices and on the other by the catalytic domain. Catalytic domain (143-410) - the active site resides in an open and accessible region in the catalytic domain at the bottom of a basket-like arrangement of 14 -helices and 8 -strands. A number of residues that are mutated in PKU are located close to the iron at the active site (e.g. thr278, glu280, pro281, trp326, phe331). Tetramerisation domain (411-452) - this consists of 2 anti-parallel -strands and a single C-terminus -helix.

The domain structures of the hydroxylases. The regulatory domains are white, the catalytic domains shaded, and the tetramerization

domains hatched. The phosphorylation sites are indicated by vertical

lines.

Phylogenetic tree of the aromatic amino acid hydroxylases. This recognizes phenylalanine hydroxylase as the ancestral hydroxylase function (from which tyrosine (TH) and tryptophan (TPH) hydroxylase functions evolved by duplications of the PAH gene). Nematodes and insects have just 3 genes (PAH, TH and TPH) located on one chromosome. The 4 or 5 genes in vertebrates are distributed on at least 2 chromosomes.

The domains comprising each subunit of the phenylalanine hydroxy-lase subunit. The regulatory domain is blue, the catalytic domain is yellow, and the tetramerization domain is green. The iron is shown as a red

sphere.

Structure of the phenylalanine hydroxylase tetramer. The model was generated from the structures of catalytic/ tetramerization domains and regulatory/catalytic domains and super-imposing the catalytic domains of the two models. The model is coloured from red (N-terminus in monomer A) to blue (C-terminus of monomer D). The iron is shown as a gray sphere in all four monomers making up the tetramer.

Alignment of the catalytic domains of PAH, TH, TP1 and TP2 from human (and Dictyostelium). The red asterisk denotes the residues coordinating the active site iron.

The active site. The iron is shown as a red sphere and the three water molecules liganded to the iron as blue spheres. Some residues that have reported PKU mutations (Thr278, Glu280, Pro281, Trp326, Phe331) and are located close to the iron in the active site, together with their interacting residues, are also shown. In B the very similar active site of tryptophan hydroxy-lase is shown.

Mutant Residue

(No)

Residue Change Site Immuno-

reactivity

Enzymic

Activity

243 arg-->term. Exon 7 <1% <1%

281 pro-->leu Exon 7 <1% <1%

408 arg-->trp Exon 12 <1% <1%

-- IVS-12 Intron 12 <1% <1%

280 glu-->lys Exon 7 <3% <3%

158 arg-->gln Exon 5 100% 10%

261 arg-->gln Exon 7 30% 30%

414 tyr-->cys Exon 12 50% 50%

Seven of the residues lining the active site that cause PKU/HPA. The main chain ribbon is coloured light green. PKU/HPA mutations have the carbon atoms in orange and residues which interact with the mutant site residues and iron ligands are in dark green.

C- trace of one monomer of phenylalanine hydroxylase. The trace is coloured yellow for residues not associated with any PKU mutations, and the active site iron is shown as a green sphere. The region coloured red consist of residues that have PKU mutations. The regions coloured blue and green have residues that show a calculated frequency of mutation higher that 10.

Active site residues that have PKU mutations associated with them: the ARG158 residue. The R158Q mutation is associated with classical PKU and is a frequent mutation in patients with PKU. ARG158 forms a salt bridge to GLU280 and a H bond with Tyr268. Both these interactions are important for conserving the shape of the active site.

Mutant Residue

(No)

Residue Change Site Immuno-

reactivity

Enzymic

Activity

243 arg-->term. Exon 7 <1% <1%

281 pro-->leu Exon 7 <1% <1%

408 arg-->trp Exon 12 <1% <1%

-- IVS-12 Intron 12 <1% <1%

280 glu-->lys Exon 7 <3% <3%

158 arg-->gln Exon 5 100% 10%

261 arg-->gln Exon 7 30% 30%

414 tyr-->cys Exon 12 50% 50%

Active site residues that have PKU mutations associated with them: the ARG252 residue. This residue forms a salt bridge with Asp315 and H bonds to the carbonyl oxygen of ALA313 and the side chain of ASP27 (in the regulatory domain). There are three PKU mutations associated with this residue: R252Q (~ 10% activity), R252G (< 1% activity) and R252W (< 1% activity).

Active site residues that have PKU mutations associated with them: the ARG261 residue. This H bonds to GLN304 and THR238. This helps to stabilize the structure of the active site. R261Q is one of the most frequent PKU mutations.

Mutant Residue

(No)

Residue Change Site Immuno-

reactivity

Enzymic

Activity

243 arg-->term. Exon 7 <1% <1%

281 pro-->leu Exon 7 <1% <1%

408 arg-->trp Exon 12 <1% <1%

-- IVS-12 Intron 12 <1% <1%

280 glu-->lys Exon 7 <3% <3%

158 arg-->gln Exon 5 100% 10%

261 arg-->gln Exon 7 30% 30%

414 tyr-->cys Exon 12 50% 50%

GLU76 is located at the interface between subunits. It is on the surface of the regulatory domain and is H bonded to HIS208 in a second monomer (as well as ASN73 just prior to GUL76 in sequence). This contact seems to be important for forming the dimer. GLU76 has two PKU mutations associated with it, E76A and E76G. Both these mutations are substitutions of a charged amino acid for surface-exposed hydrophobic residues.

ARG408 is the site of the most frequent PKU mutation (R408W). It is H bonded to LEU311 and LEU308 in the same monomer. The residue seems to be important for holding the catalytic domain together with the tetramerization domain.

Mutant Residue

(No)

Residue Change Site Immuno-

reactivity

Enzymic

Activity

243 arg-->term. Exon 7 <1% <1%

281 pro-->leu Exon 7 <1% <1%

408 arg-->trp Exon 12 <1% <1%

-- IVS-12 Intron 12 <1% <1%

280 glu-->lys Exon 7 <3% <3%

158 arg-->gln Exon 5 100% 10%

261 arg-->gln Exon 7 30% 30%

414 tyr-->cys Exon 12 50% 50%

ARG297 is predicted to be a site of frequent mutation. It is H bonded to ARG71 and GLU422 in another monomer. There are two PKU mutations: R297H and ARG297C. Both substitutions will result in disruption of the dimer-stabilizing H bonds.

GLN304 forms H bonds with TYR414 (in another monomer). The PKU mutation Q304R leads to the substitution of the polar GLN to a charged ARG. This could disrupt both H bonds and destabilize the enzyme.

The PKU-mutated residue TYR377 is associated with the regulatory domain. It H bonds to SER23 and -stacks onto TRP326.It may be important for regulating access to the active site. In the PKU mutant Y377C, the H bond would be disrupted, thus exposing the active site and destroying the effects of the regulatory domain upon substrate binding.

Summary The crystal structure of phenylalanine hydroxylase has been solved. The polypeptide consists of three domains: regulatory; catalytic; and tetramerization. It is now possible to map mutations to the structure. Active site residues that have PKU mutations associated with them include ARG158, ARG252 and ARG261. Residues involved in maintaining subunit interactions - that have PKU mutations associated with them include: GLU76 ARG297 and GLN304. ARG408 is the site of the most frequent PKU mutation (R408W). The residue seems to be important for holding the catalytic domain together with the tetramerization domain.

References Erlandsen, H. & Stevens, R. C. (1999) Mol. Gen. Metab. 68, 103-125. - Structural basis of PKU. Kim, S-W. et al., (2006) Clin. Chim. Acta 365, 279-287. - Structural & functional analysis of human phenylalanine hydroxylase. Bercovich, D. et al. (2008) J. Human Gen. 53, 407-418. - Genotype-phenotype correlations. Windahl, M. S. et al., (2008) Biochem. 47, 12087-12094 – structure of trptophan hydroxylase. http://www.pahdb.mcgill.ca/ - the PAHdb World Wide Web site.