6N1K

Full-length human phenylalanine hydroxylase (PAH) in the resting state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.057 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Biophysical characterization of full-length human phenylalanine hydroxylase provides a deeper understanding of its quaternary structure equilibrium.

Arturo, E.C.Gupta, K.Hansen, M.R.Borne, E.Jaffe, E.K.

(2019) J.Biol.Chem. 294: 10131-10145

  • DOI: 10.1074/jbc.RA119.008294

  • PubMed Abstract: 
  • Dysfunction of human phenylalanine hydroxylase (hPAH, EC 1.14.16.1) is the primary cause of phenylketonuria, the most common inborn error of amino acid metabolism. The dynamic domain rearrangements of this multimeric protein have thwarted structural ...

    Dysfunction of human phenylalanine hydroxylase (hPAH, EC 1.14.16.1) is the primary cause of phenylketonuria, the most common inborn error of amino acid metabolism. The dynamic domain rearrangements of this multimeric protein have thwarted structural study of the full-length form for decades, until now. In this study, a tractable C29S variant of hPAH (C29S) yielded a 3.06 Å resolution crystal structure of the tetrameric resting-state conformation. We used size-exclusion chromatography in line with small-angle X-ray scattering (SEC-SAXS) to analyze the full-length hPAH solution structure both in the presence and absence of Phe, which serves as both substrate and allosteric activator. Allosteric Phe binding favors accumulation of an activated PAH tetramer conformation, which is biophysically distinct in solution. Protein characterization with enzyme kinetics and intrinsic fluorescence revealed that the C29S variant and hPAH are otherwise equivalent in their response to Phe, further supported by their behavior on various chromatography resins and by analytical ultracentrifugation (AUC). Modeling of resting-state and activated forms of C29S against SAXS data with available structural data created and evaluated several new models for the transition between the architecturally distinct conformations of PAH and highlighted unique intra- and inter-subunit interactions. Three best-fitting alternate models all placed the allosteric Phe-binding module 8-10 Å farther from the tetramer center than do all previous models. The structural insights into allosteric activation of hPAH reported here may help inform ongoing efforts to treat phenylketonuria with novel therapeutic approaches.


    Organizational Affiliation

    Scripps Research Institute, United States.,Developmental Therapeutics, Fox Chase Cancer Center, United States.,Sidney Kimmel Medical College, United States.,Janssen Research & Development, United States.,Perelman School of Medicine, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phenylalanine-4-hydroxylase
A, B, C, D
451Homo sapiensMutation(s): 1 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B, C, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 72.437α = 90.00
b = 202.640β = 90.30
c = 72.574γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited States1R01NS100081-03

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-07-10
    Type: Data collection, Database references