6HYC

The structure of full-length human phenylalanine hydroxylase in complex with the cofactor and negative regulator tetrahydrobiopterin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.262 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.USA 116: 11229-11234

  • DOI: 10.1073/pnas.1902639116
  • Primary Citation of Related Structures:  

  • 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 fro ...

    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.,Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain.,Department of Biomedicine, University of Bergen, 5009 Bergen, Norway; aurora.martinez@uib.no xjuan@iqfr.csic.es.,Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phenylalanine-4-hydroxylase
D, A, C, B
452Homo sapiensMutation(s): 0 
Gene Names: PAH
EC: 1.14.16.1
Find proteins for P00439 (Homo sapiens)
Go to Gene View: PAH
Go to UniProtKB:  P00439
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H4B
Query on H4B

Download SDF File 
Download CCD File 
B, C, D
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.262 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.940α = 90.00
b = 101.368β = 90.00
c = 203.543γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
MoRDaphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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