Crystal structure of C. violaceum phenylalanine hydroxylase D139E mutation

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

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A conserved acidic residue in phenylalanine hydroxylase contributes to cofactor affinity and catalysis.

Ronau, J.A.Paul, L.N.Fuchs, J.E.Liedl, K.R.Abu-Omar, M.M.Das, C.

(2014) Biochemistry 53: 6834-6848

  • DOI: https://doi.org/10.1021/bi500734h
  • Primary Citation of Related Structures:  
    4Q3W, 4Q3X, 4Q3Y, 4Q3Z

  • PubMed Abstract: 

    The catalytic domains of aromatic amino acid hydroxylases (AAAHs) contain a non-heme iron coordinated to a 2-His-1-carboxylate facial triad and two water molecules. Asp139 from Chromobacterium violaceum PAH (cPAH) resides within the second coordination sphere and contributes key hydrogen bonds with three active site waters that mediate its interaction with an oxidized form of the cofactor, 7,8-dihydro-l-biopterin, in crystal structures. To determine the catalytic role of this residue, various point mutants were prepared and characterized. Our isothermal titration calorimetry (ITC) analysis of iron binding implies that polarity at position 139 is not the sole criterion for metal affinity, as binding studies with D139E suggest that the size of the amino acid side chain also appears to be important. High-resolution crystal structures of the mutants reveal that Asp139 may not be essential for holding the bridging water molecules together, because many of these waters are retained even in the Ala mutant. However, interactions via the bridging waters contribute to cofactor binding at the active site, interactions for which charge of the residue is important, as the D139N mutant shows a 5-fold decrease in its affinity for pterin as revealed by ITC (compared to a 16-fold loss of affinity in the case of the Ala mutant). The Asn and Ala mutants show a much more pronounced defect in their kcat values, with nearly 16- and 100-fold changes relative to that of the wild type, respectively, indicating a substantial role of this residue in stabilization of the transition state by aligning the cofactor in a productive orientation, most likely through direct binding with the cofactor, supported by data from molecular dynamics simulations of the complexes. Our results indicate that the intervening water structure between the cofactor and the acidic residue masks direct interaction between the two, possibly to prevent uncoupled hydroxylation of the cofactor before the arrival of phenylalanine. It thus appears that the second-coordination sphere Asp residue in cPAH, and, by extrapolation, the equivalent residue in other AAAHs, plays a role in fine-tuning pterin affinity in the ground state via deformable interactions with bridging waters and assumes a more significant role in the transition state by aligning the cofactor through direct hydrogen bonding.

  • Organizational Affiliation

    Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phenylalanine-4-hydroxylase297Chromobacterium violaceum ATCC 12472Mutation(s): 1 
Gene Names: phhACV_3180
Find proteins for P30967 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757))
Explore P30967 
Go to UniProtKB:  P30967
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30967
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.003α = 76.66
b = 38.673β = 72.86
c = 47.813γ = 85.6
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description