Crystallographic structure of the catalytic domain of Human Phenylalanine Hydroxylase (hPAH CD) in complex with iron at 1.6 Angstrom

Experimental Data Snapshot

  • Resolution: 1.67 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

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Structure of full-length human phenylalanine hydroxylase in complex with tetrahydrobiopterin.

Flydal, M.I.Alcorlo-Pages, M.Johannessen, F.G.Martinez-Caballero, S.Skjærven, L.Fernandez-Leiro, R.Martinez, A.Hermoso, J.A.

(2019) Proc Natl Acad Sci U S A 116: 11229-11234

  • DOI: https://doi.org/10.1073/pnas.1902639116
  • Primary Citation of Related Structures:  
    6HPO, 6HYC

  • PubMed 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 retardation if untreated. Some patients benefit from supplementation with a synthetic formulation of the cofactor tetrahydrobiopterin (BH 4 ) that partly acts as a pharmacological chaperone. Here we present structures of full-length human PAH (hPAH) both unbound and complexed with BH 4 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 4 BH 4 forms several H-bonds with the N-terminal autoregulatory tail but is far from the catalytic Fe II Upon BH 4 binding a polar and salt-bridge interaction network links the three PAH domains, explaining the stability conferred by BH 4 Importantly, BH 4 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 4 reveals a highly dynamic conformation for the tetramers. Structural analyses of the hPAH:BH 4 subunits revealed that the substrate-induced movement of Tyr138 into the active site could be coupled to the displacement of BH 4 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.

  • Organizational Affiliation

    Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain; aurora.martinez@uib.no xjuan@iqfr.csic.es.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phenylalanine-4-hydroxylase452Homo sapiensMutation(s): 0 
Gene Names: PAH
UniProt & NIH Common Fund Data Resources
Find proteins for P00439 (Homo sapiens)
Explore P00439 
Go to UniProtKB:  P00439
PHAROS:  P00439
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00439
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FE

Download Ideal Coordinates CCD File 
B [auth A]FE (III) ION
Experimental Data & Validation

Experimental Data

  • Resolution: 1.67 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.856α = 90
b = 107.549β = 90
c = 124.016γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2014-59389-P and BFU2017-90030-P to JAH
Research Council of NorwayNorwayPrograms Forny (248889/O30) and FRIMEDBIO (261826) to AM

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-06-19
    Changes: Data collection, Database references