|Entry||Database: PDB / ID: 6hpo|
|Title||Crystallographic structure of the catalytic domain of Human Phenylalanine Hydroxylase (hPAH CD) in complex with iron at 1.6 Angstrom|
|Keywords||OXIDOREDUCTASE / Tetrahydrobiopterin / amino acid hydroxylases / phenylketonuria / allosteric regulation / METAL BINDING PROTEIN / oxidoreductase|
|Function / homology|
Function and homology information
rt:r-hsa-71182: / Phenylketonuria / ec:220.127.116.11: / phenylalanine 4-monooxygenase activity / tyrosine biosynthetic process / catecholamine biosynthetic process / neurotransmitter biosynthetic process / L-phenylalanine catabolic process / cellular amino acid biosynthetic process / iron ion binding / cytosol
Tyrosine 3-monooxygenase-like / Aromatic amino acid hydroxylase superfamily / ACT domain profile. / Biopterin-dependent aromatic amino acid hydroxylase family profile. / Biopterin-dependent aromatic amino acid hydroxylases signature. / ACT domain / Biopterin-dependent aromatic amino acid hydroxylase / Aromatic amino acid hydroxylase / ACT domain / Phenylalanine-4-hydroxylase, tetrameric form ...Tyrosine 3-monooxygenase-like / Aromatic amino acid hydroxylase superfamily / ACT domain profile. / Biopterin-dependent aromatic amino acid hydroxylase family profile. / Biopterin-dependent aromatic amino acid hydroxylases signature. / ACT domain / Biopterin-dependent aromatic amino acid hydroxylase / Aromatic amino acid hydroxylase / ACT domain / Phenylalanine-4-hydroxylase, tetrameric form / Aromatic amino acid hydroxylase, iron/copper binding site / Eukaryotic phenylalanine-4-hydroxylase, catalytic domain / Aromatic amino acid hydroxylase, C-terminal / Aromatic amino acid monoxygenase, C-terminal domain superfamily
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å|
|Authors||Alcorlo Pages, M. / Innselset Flydal, M.|
|Funding support||Spain , Norway , 2件 |
|Citation||Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019|
Title: Structure of full-length human phenylalanine hydroxylase in complex with tetrahydrobiopterin.
Authors: Marte Innselset Flydal / Martín Alcorlo-Pagés / Fredrik Gullaksen Johannessen / Siseth Martínez-Caballero / Lars Skjærven / Rafael Fernandez-Leiro / Aurora Martinez / Juan A Hermoso /
Abstract: Phenylalanine hydroxylase (PAH) is a key enzyme in the catabolism of phenylalanine, and mutations in this enzyme cause phenylketonuria (PKU), a genetic disorder that leads to brain damage and mental ...Phenylalanine hydroxylase (PAH) is a key enzyme in the catabolism of phenylalanine, and mutations in this enzyme cause phenylketonuria (PKU), a genetic disorder that leads to brain damage and mental retardation if untreated. Some patients benefit from supplementation with a synthetic formulation of the cofactor tetrahydrobiopterin (BH) that partly acts as a pharmacological chaperone. Here we present structures of full-length human PAH (hPAH) both unbound and complexed with BH in the precatalytic state. Crystal structures, solved at 3.18-Å resolution, show the interactions between the cofactor and PAH, explaining the negative regulation exerted by BH BH forms several H-bonds with the N-terminal autoregulatory tail but is far from the catalytic Fe Upon BH binding a polar and salt-bridge interaction network links the three PAH domains, explaining the stability conferred by BH Importantly, BH binding modulates the interaction between subunits, providing information about PAH allostery. Moreover, we also show that the cryo-EM structure of hPAH in absence of BH reveals a highly dynamic conformation for the tetramers. Structural analyses of the hPAH:BH subunits revealed that the substrate-induced movement of Tyr138 into the active site could be coupled to the displacement of BH from the precatalytic toward the active conformation, a molecular mechanism that was supported by site-directed mutagenesis and targeted molecular dynamics simulations. Finally, comparison of the rat and human PAH structures show that hPAH is more dynamic, which is related to amino acid substitutions that enhance the flexibility of hPAH and may increase the susceptibility to PKU-associated mutations.
SummaryFull reportAbout validation report
|Date||Deposition: Sep 21, 2018 / Release: Jun 5, 2019|
|Structure viewer||Molecule: |
Downloads & links
|#1: Protein/peptide|| |
Mass: 51928.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAH / Production host: Escherichia coli (E. coli) / References: UniProt: P00439, EC: 18.104.22.168
|#2: Chemical|| ChemComp-FE / |
|#3: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.48 Å3/Da / Density % sol: 50.35 %|
|Crystal grow||Temperature: 291 K / Method: vapor diffusion / Details: 40 mM PIPES, 20% PEG 2000, pH 6.8|
|Diffraction||Mean temperature: 100 K / Serial crystal experiment: N|
|Diffraction source||Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å|
|Detector||Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 1, 2018|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.9792 Å / Relative weight: 1|
|Reflection||Resolution: 1.67→32.77 Å / Num. obs: 51389 / % possible obs: 99.96 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.026 / Net I/σ(I): 16.2|
|Reflection shell||Resolution: 1.67→1.73 Å / Rmerge(I) obs: 1.921 / Num. unique obs: 2603 / Rpim(I) all: 0.574|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: 4ANP
Resolution: 1.67→32.77 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.41
|Solvent computation||Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å|
|Refinement step||Cycle: LAST / Resolution: 1.67→32.77 Å|
|Refine LS restraints|
Refinement-ID: X-RAY DIFFRACTION
|LS refinement shell|
Refinement-ID: X-RAY DIFFRACTION / % reflection obs: 100 %
|Refinement TLS params.||Method: refined / Origin x: 0.1353 Å / Origin y: 24.8754 Å / Origin z: 9.606 Å|
|Refinement TLS group||Selection details: all|
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