Phenylalanine hydroxylase

PAH
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 1DMW, 1J8T, 1J8U, 1KW0, 1LRM, 1MMK, 1MMT, 1TDW, 1TG2, 2PAH, 3PAH, 4ANP, 5PAH, 6PAH, 5FII
Identifiers
Aliases	PAH, PH, PKU, PKU1, phenylalanine hydroxylase
External IDs	OMIM: 612349 MGI: 97473 HomoloGene: 234 GeneCards: PAH
Targeted by Drug
fenclonine[1]
Gene ontology Molecular function • iron ion binding • amino acid binding • phenylalanine 4-monooxygenase activity • metal ion binding • monooxygenase activity • catalytic activity • oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced pteridine as one donor, and incorporation of one atom of oxygen • oxidoreductase activity Cellular component • cytosol • extracellular exosome Biological process • catecholamine biosynthetic process • neurotransmitter biosynthetic process • L-phenylalanine catabolic process • cellular amino acid biosynthetic process • aromatic amino acid family metabolic process • metabolic process • oxidation-reduction process Sources:Amigo / QuickGO
RNA expression pattern
More reference expression data
Orthologs
Species	Human	Mouse
Entrez	5053	18478
Ensembl	ENSG00000171759	ENSMUSG00000020051
UniProt	P00439	P16331
RefSeq (mRNA)	NM_000277	NM_008777
RefSeq (protein)	NP_000268.1	NP_032803.2
Location (UCSC)	Chr 12: 102.84 – 102.96 Mb	Chr 10: 87.52 – 87.58 Mb
PubMed search	[2]	[3]
Wikidata

Phenylalanine hydroxylase (PAH) (EC 1.14.16.1) is an enzyme that catalyzes the hydroxylation of the aromatic side-chain of phenylalanine to generate tyrosine. PAH is one of three members of the biopterin-dependent aromatic amino acid hydroxylases, a class of monooxygenase that uses tetrahydrobiopterin (BH₄, a pteridine cofactor) and a non-heme iron for catalysis. During the reaction, molecular oxygen is heterolytically cleaved with sequential incorporation of one oxygen atom into BH₄ and phenylalanine substrate.^[4]

Reaction catalyzed by PAH

Phenylalanine hydroxylase is the rate-limiting enzyme of the metabolic pathway that degrades excess phenylalanine. Research on phenylalanine hydroxylase by Seymour Kaufman led to the discovery of tetrahydrobiopterin as a biological cofactor.^[5] The enzyme is also interesting from a human health perspective because mutations in PAH, the encoding gene, can lead to phenylketonuria, a severe metabolic disorder.

Enzyme mechanism

The reaction is thought to proceed through the following steps:

1. formation of a Fe(II)-O-O-BH₄ bridge.
2. heterolytic cleavage of the O-O bond to yield the ferryl oxo hydroxylating intermediate Fe(IV)=O
3. attack on Fe(IV)=O to hydroxylate phenylalanine substrate to tyrosine.^[6]

PAH mechanism, part I

Formation and cleavage of the iron-peroxypterin bridge. Although evidence strongly supports Fe(IV)=O as the hydroxylating intermediate,^[7] the mechanistic details underlying the formation of the Fe(II)-O-O-BH₄ bridge prior to heterolytic cleavage remain controversial. Two pathways have been proposed based on models that differ in the proximity of the iron to the pterin cofactor and the number of water molecules assumed to be iron-coordinated during catalysis. According to one model, an iron dioxygen complex is initially formed and stabilized as a resonance hybrid of Fe²⁺O₂ and Fe³⁺O₂⁻. The activated O₂ then attacks BH₄, forming a transition state characterized by charge separation between the electron-deficient pterin ring and the electron-rich dioxygen species.^[8] The Fe(II)-O-O-BH4 bridge is subsequently formed. On the other hand, formation of this bridge has been modeled assuming that BH4 is located in iron's first coordination shell and that the iron is not coordinated to any water molecules. This model predicts a different mechanism involving a pterin radical and superoxide as critical intermediates.^[9] Once formed, the Fe(II)-O-O-BH₄ bridge is broken through heterolytic cleavage of the O-O bond to Fe(IV)=O and 4a-hydroxytetrahydrobiopterin; thus, molecular oxygen is the source of both oxygen atoms used to hydroxylate the pterin ring and phenylalanine.

PAH mechanism, part II

Hydroxylation of phenylalanine by ferryl oxo intermediate. Because the mechanism involves a Fe(IV)=O (as opposed to a peroxypterin) hydroxylating intermediate, oxidation of the BH₄ cofactor and hydroxylation of phenylalanine can be decoupled, resulting in unproductive consumption of BH4 and formation of H2O2.^[6] When productive, though, the Fe(IV)=O intermediate is added to phenylalanine in an electrophilic aromatic substitution reaction that reduces iron from the ferryl to the ferrous state.^[6] Although initially an arene oxide or radical intermediate was proposed, analyses of the related tryptophan and tyrosine hydroxylases have suggested that the reaction instead proceeds through a cationic intermediate that requires Fe(IV)=O to be coordinated to a water ligand rather than a hydroxo group.^[6][10] This cationic intermediate subsequently undergoes a 1,2-hydride NIH shift, yielding a dienone intermediate that then tautomerizes to form the tyrosine product.^[11] The pterin cofactor is regenerated by hydration of the carbinolamine product of PAH to quinonoid dihydrobiopterin (qBH₂), which is then reduced to BH₄.^[12]

Enzyme regulation

PAH is proposed to use the morpheein model of allosteric regulation.^[13][14]

Mammalian PAH exists in an equilibrium consisting of tetramers of two distinct architectures, with one or more dimeric forms as part of the equilibrium. This behavior is consistent with a dissociative allosteric mechanism.^[14]

Many studies suggest that mammalian PAH shows behavior comparable to porphobilinogen synthase (PBGS), wherein a variety of factors such as pH and ligand binding are reported to affect enzyme activity and protein stability.^[14]

Structure

The PAH monomer (51.9 kDa) consists of three distinct domains: a regulatory N-terminal domain (residues 1-117), the catalytic domain (residues 118-427), and a C-terminal domain (residues 428-453) responsible for oligomerization of identical monomers. Extensive crystallographic analysis has been performed, especially on the pterin- and iron-coordinated catalytic domain to examine the active site. The structure of the N-terminal regulatory domain has also been determined, and together with the solved structure of the homologous tyrosine hydroxylase C-terminal tetramerization domain, a structural model of tetrameric PAH has been proposed.^[12]

Model of the active site of PAH bound to BH4, ferrous, and a phenylalanine analogue. (from PDB 1KW0) Phenylalanine analogue, BH4, iron, Fe(II)-coordinated His and Glu residues

Catalytic domain

Solved crystal structures of the catalytic domain indicate that the active site consists of an open and spacious pocket lined primarily by hydrophobic residues, though three glutamic acid residues, two histidines, and a tyrosine are also present and iron-binding.^[12] Contradictory evidence exists about the coordination state of the ferrous atom and its proximity to BH4 within the active site. According to crystallographic analysis, Fe(II) is coordinated by water, His285, His290, and Glu330 (a 2-his-1-carboxylate facial triad arrangement) with octahedral geometry.^[15] Inclusion of a Phe analogue in the crystal structure changes both iron from a six- to a five-coordinated state involving a single water molecule and bidentate coordination to Glu330 and opening a site for oxygen to bind. BH4 is concommitantly shifted toward the iron atom, although the pterin cofactor remains in the second coordination sphere.^[16] On the other hand, a competing model based on NMR and molecular modeling analyses suggests that all coordinated water molecules are forced out of the active site during the catalytic cycle while BH4 becomes directly coordinated to iron.^[17] As discussed above, resolving this discrepancy will be important for determining the exact mechanism of PAH catalysis.

N-terminal regulatory domain

The regulatory nature of the N-terminal domain (residues 1-117) is conferred by its structural flexibility.^[18] Hydrogen/deuterium exchanges analysis indicates that allosteric binding of Phe globally alters the conformation of PAH such that the active site is less occluded as the interface between the regulatory and catalytic domains is increasingly exposed to solvent.^[18][19][20] This observation is consistent with kinetic studies, which show an initially low rate of tyrosine formation for full-length PAH. This lag time is not observed, however, for a truncated PAH lacking the N-terminal domain or if the full-length enzyme is pre-incubated with Phe. Deletion of the N-terminal domain also eliminates the lag time while increasing the affinity for Phe by nearly two-fold; no difference is observed in the V_max or K_m for the tetrahydrobiopterin cofactor.^[21] Additional regulation is provided by Ser16; phosphorylation of this residue does not alter enzyme conformation but does reduce the concentration of Phe required for allosteric activation.^[20] This N-terminal regulatory domain is not observed in bacterial PAHs but shows considerable structural homology to the regulatory domain of phosphogylcerate dehydrogenase, an enzyme in the serine biosynthetic pathway.^[20]

Tetramerization domain

Prokaryotic PAH is monomeric, whereas eukaryotic PAH exists in an equilibrium between homotetrameric and homodimeric forms.^[6][12] The dimerization interface is composed of symmetry-related loops that link identical monomers, while the overlapping C-terminal tetramerization domain mediates the association of conformationally distinct dimers that are characterized by a different relative orientation of the catalytic and tetramerization domains (Flatmark, Erlandsen). The resulting distortion of the tetramer symmetry is evident in the differential surface area of the dimerization interfaces and distinguishes PAH from the tetramerically symmetrical tyrosine hydroxylase.^[12] A domain-swapping mechanism has been proposed to mediate formation of the tetramer from dimers, in which C-terminal alpha-helixes mutually alter their conformation around a flexible C-terminal five-residue hinge region to form a coiled-coil structure, shifting equilibrium toward the tetrameric form.^[6][12][22] Although both the homodimeric and homotetrameric forms of PAH are catalytically active, the two exhibit differential kinetics and regulation. In addition to reduced catalytic efficiency, the dimer does not display positive cooperativity toward L-Phe (which at high concentrations activates the enzyme), suggesting that L-Phe allosterically regulates PAH by influencing dimer-dimer interaction.^[22]

Biological function

PAH is a critical enzyme in phenylalanine metabolism and catalyzes the rate-limiting step in its complete catabolism to carbon dioxide and water.^[12][23] Regulation of flux through phenylalanine-associated pathways is critical in mammalian metabolism, as evidenced by the toxicity of high plasma levels of this amino acid observed in phenylketonuria (see below.) The principal source of phenylalanine is ingested proteins but relatively little of this pool is used for protein synthesis.^[23] Instead, the majority of ingested phenylalanine is catabolized through PAH to form tyrosine; addition of the hydroxyl group allows for the benzene ring to be broken in subsequent catabolic steps. Transamination to phenylpyruvate, whose metabolites are excreted in the urine, represents another pathway of phenylalanine turnover, but catabolism through PAH predominates.^[23]

In humans, this enzyme is expressed both in the liver and the kidney, and there is some indication that it may be differentially regulated in these tissues.^[24] PAH is unusual among the aromatic amino acid hydroxylases for its involvement in catabolism; tyrosine and tryptophan hydroxylases, on the other hand, are primarily expressed in the central nervous system and catalyze rate-limiting steps in neurotransmitter/hormone biosynthesis.^[12]

Disease relevance

Deficiency in PAH activity due to mutations in the PAH gene causes hyperphenylalaninemia (HPA), and when blood phenylalanine levels increase above 20 times the normal concentration, the metabolic disease phenylketonuria (PKU) results.^[23] PKU is both genotypically and phenotypically heterogeneous: Over 300 distinct pathological mutants have been identified, the majority of which correspond to missense mutations that map to the catalytic domain.^[12][15] When a cohort of identified PAH mutants were expressed in recombinant systems, the enzymes displayed altered kinetic behavior and/or reduced stability, consistent with structural mapping of these mutations to both the catalytic and tetramerization domains of the enzyme.^[12] BH4₄ has been administered as a pharmacological treatment and has been shown to reduce blood levels of phenylalanine for a segment of PKU patients whose genotypes lead to some residual PAH activity but have no defect in BH4₄ synthesis or regeneration. Follow-up studies suggest that in the case of certain PAH mutants, excess BH4₄ acts as a pharmacological chaperone to stabilize mutant enzymes with disrupted tetramer assembly and increased sensitivity to proteolytic cleavage and aggregation.^[25] Mutations that have been identified in the PAH locus are documented at the Phenylalanine Hydroxylase Locus Knowledgbase (PAHdb, http://www.pahdb.mcgill.ca/).

Since phenylketonurea can cause irreversible damage, it is imperative that deficiencies in the Phenylalanine Hydroxylase are determined early on in development. One method is a post-parturition screening test known as the Guthrie Test. The common method is via drawing blood from a small needle prick at the heel of the newborn and testing it for phenylketonurea, indicative of a PH deficiency. Placing the individual on a low phenylalanine, high tyrosine diet can help prevent any long-term damage to their development.

Related enzymes

Phenylalanine hydroxylase is closely related to two other enzymes:

• tryptophan hydroxylase (EC number 1.14.16.4), which controls levels of serotonin in the brain and the gastrointestinal tract
• tyrosine hydroxylase (EC number 1.14.16.2), which controls levels of dopamine, epinephrine, and norepinephrine in the brain and the adrenal medulla.

The three enzymes are homologous, that is, are thought to have evolved from the same ancient hydroxylase.

References

Further reading

External links

• GeneReviews/NCBI/NIH/UW entry on Phenylalanine Hydroxylase Deficiency
• Locus-specific database of the human phenylalanine hydroxylase gene variants
• Molecule of the Month: Phenylalanine Hydroxylase

PDB gallery
1dmw: CRYSTAL STRUCTURE OF DOUBLE TRUNCATED HUMAN PHENYLALANINE HYDROXYLASE WITH BOUND 7,8-DIHYDRO-L-BIOPTERIN  1j8t: Catalytic Domain of Human Phenylalanine Hydroxylase Fe(II)  1j8u: Catalytic Domain of Human Phenylalanine Hydroxylase Fe(II) in Complex with Tetrahydrobiopterin  1kw0: Catalytic Domain of Human Phenylalanine Hydroxylase (Fe(II)) in Complex with Tetrahydrobiopterin and Thienylalanine  1lrm: Crystal structure of binary complex of the catalytic domain of human phenylalanine hydroxylase with dihydrobiopterin (BH2)  1mmk: Crystal structure of ternary complex of the catalytic domain of human phenylalanine hydroxylase ((FeII)) complexed with tetrahydrobiopterin and thienylalanine  1mmt: Crystal structure of ternary complex of the catalytic domain of human phenylalanine hydroxylase (Fe(II)) complexed with tetrahydrobiopterin and norleucine  1pah: HUMAN PHENYLALANINE HYDROXYLASE DIMER, RESIDUES 117-424  1phz: STRUCTURE OF PHOSPHORYLATED PHENYLALANINE HYDROXYLASE  1tdw: Crystal structure of double truncated human phenylalanine hydroxylase BH4-responsive PKU mutant A313T.  1tg2: Crystal structure of phenylalanine hydroxylase A313T mutant with 7,8-dihydrobiopterin bound  2pah: TETRAMERIC HUMAN PHENYLALANINE HYDROXYLASE  2phm: STRUCTURE OF PHENYLALANINE HYDROXYLASE DEPHOSPHORYLATED  3pah: HUMAN PHENYLALANINE HYDROXYLASE CATALYTIC DOMAIN DIMER WITH BOUND ADRENALINE INHIBITOR  4pah: HUMAN PHENYLALANINE HYDROXYLASE CATALYTIC DOMAIN DIMER WITH BOUND NOR-ADRENALINE INHIBITOR  5pah: HUMAN PHENYLALANINE HYDROXYLASE CATALYTIC DOMAIN DIMER WITH BOUND DOPAMINE INHIBITOR  6pah: HUMAN PHENYLALANINE HYDROXYLASE CATALYTIC DOMAIN DIMER WITH BOUND L-DOPA (3,4-DIHYDROXYPHENYLALANINE) INHIBITOR