1BKW

p-Hydroxybenzoate hydroxylase (phbh) mutant with cys116 replaced by ser (c116s) and arg44 replaced by lys (r44k), in complex with fad and 4-hydroxybenzoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure and function of mutant Arg44Lys of 4-hydroxybenzoate hydroxylase implications for NADPH binding.

Eppink, M.H.Schreuder, H.A.Van Berkel, W.J.

(1995) Eur J Biochem 231: 157-165

  • DOI: 10.1111/j.1432-1033.1995.0157f.x
  • Primary Citation of Related Structures:  
    1BKW

  • PubMed Abstract: 
  • Arg44, located at the si-face side of the flavin ring in 4-hydroxybenzoate hydroxylase, was changed to lysine by site-specific mutagenesis. Crystals of [R44K]4-hydroxybenzoate hydroxylase complexed with 4-hydroxybenzoate diffract to 0.22-nm resolution. The structure of [R44K]4-hydroxybenzoate hydroxylase is identical to the wild-type enzyme except for local changes in the vicinity of the mutation ...

    Arg44, located at the si-face side of the flavin ring in 4-hydroxybenzoate hydroxylase, was changed to lysine by site-specific mutagenesis. Crystals of [R44K]4-hydroxybenzoate hydroxylase complexed with 4-hydroxybenzoate diffract to 0.22-nm resolution. The structure of [R44K]4-hydroxybenzoate hydroxylase is identical to the wild-type enzyme except for local changes in the vicinity of the mutation. The peptide unit between Ile43 and Lys44 is flipped by about 180 degrees in 50% of the molecules. The phi, psi angles in both the native and flipped conformation are outside the allowed regions and indicate a strained conformation. [R44K]4-Hydroxybenzoate hydroxylase has a decreased affinity for the flavin prosthetic group. This is ascribed to the lost interactions between the side chain of Arg44 and the diphosphoribose moiety of the FAD. The replacement of Arg44 by Lys does not change the position of the flavin ring which occupies the same interior position as in wild type. [R44K]4-Hydroxybenzoate hydroxylase fully couples flavin reduction to substrate hydroxylation. Stopped-flow kinetics showed that the effector role of 4-hydroxybenzoate is largely conserved in the mutant. Replacement of Arg44 by Lys however affects NADPH binding, resulting in a low yield of the charge-transfer species between reduced flavin and NADP+. It is inferred from these data that Arg44 is indispensable for optimal catalysis.


    Related Citations: 
    • Crystal Structure of P-Hydroxybenzoate Hydroxylase Reconstituted with the Modified FAD Present in Alcohol Oxidase from Methyloprophic Yeasts: Evidence for an Arabinoflavin
      Van Berkel, W.J., Eppink, M.H., Schreuder, H.A.
      (1994) Protein Sci 3: 2245
    • Crystal Structures of Wild-Type p-Hydroxybenzoate Hydroxylase Complexed with 4- Aminobenzoate, 2,4-Dihydroxybenzoate, and 2-Hydroxy-4-Aminobenzoate and the Tyr222Ala Mutant Complexed with 2-Hydroxy-4-Aminobenzoate. Evidence for a Proton Channel and a New Binding Mode of the Flavin Ring
      Schreuder, H.A., Mattevi, A., Obmolova, G., Kalk, K.H., Hol, W.G., Van Der Bolt, F.J., Van Berkel, W.J.
      (1994) Biochemistry 33: 10161
    • Crystal Structure of the Reduced Form of P-Hydroxybenzoate Hydroxylase Refined at 2.3 Angstroms Resolution
      Schreuder, H.A., Van Der Laan, J.M., Swarte, M.B., Kalk, K.H., Hol, W.G., Drenth, J.
      (1992) Proteins 14: 178
    • Engineering of the Microheterogeneity-Resistant P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens
      Eschrich, K., Van Berkel, W.J., Westphal, A.H., De Kok, A., Mattevi, A., Obmolova, G., Kalk, H., Hol, W.G.
      (1990) FEBS Lett 277: 197
    • Crystal Structure of the P-Hydroxybenzoate Hydroxylase-Substrate Complex Refined at 1.9 Angstroms Resolution. Analysis of the Enzyme-Substrate and Enzyme-Product Complexes
      Schreuder, H.A., Prick, P.A., Wierenga, R.K., Vriend, G., Wilson, K.S., Hol, W.G., Drenth, J.
      (1989) J Mol Biol 208: 679
    • The Coenzyme Analogue Adenosine 5-Diphosphoribose Displaces FAD in the Active Site of P-Hydroxybenzoate Hydroxylase. An X-Ray Crystallographic Investigation
      Van Der Laan, J.M., Schreuder, H.A., Swarte, M.B., Wierenga, R.K., Kalk, K.H., Hol, W.G., Drenth, J.
      (1989) Biochemistry 28: 7199
    • Crystal Structure of P-Hydroxybenzoate Hydroxylase Complexed with its Reaction Product 3,4-Dihydroxybenzoate
      Schreuder, H.A., Van Der Laan, J.M., Hol, W.G., Drenth, J.
      (1988) J Mol Biol 199: 637
    • Crystal Structure of P-Hydroxybenzoate Hydroxylase
      Wierenga, R.K., De Jong, R.J., Kalk, K.H., Hol, W.G., Drenth, J.
      (1979) J Mol Biol 131: 55
    • Crystallization and Preliminary X-Ray Investigation of P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens
      Drenth, J., Hol, W.G.J., Wierenga, R.K.
      (1975) J Biol Chem 250: 5268

    Organizational Affiliation

    Department of Biochemistry, Agricultural University, Wageningen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (P-HYDROXYBENZOATE HYDROXYLASE)A394Pseudomonas fluorescensMutation(s): 2 
Gene Names: pobA
EC: 1.14.13.2
UniProt
Find proteins for P00438 (Pseudomonas fluorescens)
Explore P00438 
Go to UniProtKB:  P00438
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
PHB
Query on PHB

Download Ideal Coordinates CCD File 
C [auth A]P-HYDROXYBENZOIC ACID
C7 H6 O3
FJKROLUGYXJWQN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.7α = 90
b = 146.4β = 90
c = 88.5γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XSCALEdata scaling
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-07-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance