1YKP

Protocatechuate 3,4-Dioxygenase Y408H mutant bound to DHB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Roles of the equatorial tyrosyl iron ligand of protocatechuate 3,4-dioxygenase in catalysis

Valley, M.P.Brown, C.K.Burk, D.L.Vetting, M.W.Ohlendorf, D.H.Lipscomb, J.D.

(2005) Biochemistry 44: 11024-11039

  • DOI: 10.1021/bi050902i
  • Primary Citation of Related Structures:  
    1YKP, 1YKO, 1YKN, 1YKM, 1YKL, 1YKK

  • PubMed Abstract: 
  • The active site Fe(III) of protocatechuate 3,4-dioxygenase (3,4-PCD) from Pseudomonas putida is ligated axially by Tyr447 and His462 and equatorially by Tyr408, His460, and OH(-). Tyr447 and OH(-) are displaced as protocatechuate (3,4-dihydroxybenzoate, PCA) chelates the iron and appear to serve as in situ bases to promote this process ...

    The active site Fe(III) of protocatechuate 3,4-dioxygenase (3,4-PCD) from Pseudomonas putida is ligated axially by Tyr447 and His462 and equatorially by Tyr408, His460, and OH(-). Tyr447 and OH(-) are displaced as protocatechuate (3,4-dihydroxybenzoate, PCA) chelates the iron and appear to serve as in situ bases to promote this process. The role(s) of Tyr408 is (are) explored here using mutant enzymes that exhibit less than 0.1% wild-type activity. The X-ray crystal structures of the mutants and their PCA complexes show that the new shorter residues in the 408 position cannot ligate the iron and instead interact with the iron through solvents. Moreover, PCA binds as a monodentate rather than a bidentate ligand, and Tyr447 fails to dissociate. Although the new residues at position 408 do not directly bind to the iron, large changes in the spectroscopic and catalytic properties are noted among the mutant enzymes. Resonance Raman features show that the Fe-O bond of the monodentate 4-hydroxybenzoate (4HB) inhibitor complex is significantly stronger in the mutants than in wild-type 3,4-PCD. Transient kinetic studies show that PCA and 4HB bind to 3,4-PCD in a fast, reversible step followed by a step in which coordination to the metal occurs; the latter process is at least 50-fold slower in the mutant enzymes. It is proposed that, in wild-type 3,4-PCD, the Lewis base strength of Tyr408 lowers the Lewis acidity of the iron to foster the rapid exchange of anionic ligands during the catalytic cycle. Accordingly, the increase in Lewis acidity of the iron caused by substitution of this residue by solvent tends to make the iron substitution inert. Tyr447 cannot be released to allow formation of the usual dianionic PCA chelate complex with the active site iron, and the rate of electrophilic attack by O(2) becomes rate limiting overall. The structures of the PCA complexes of these mutant enzymes show that hydrogen-bonding interactions between the new solvent ligand and the new second-sphere residue in position 408 allow this residue to significantly influence the spectroscopic and kinetic properties of the enzymes.


    Organizational Affiliation

    Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protocatechuate 3,4-dioxygenase alpha chainA, C, E, G, I, K200Pseudomonas putidaMutation(s): 0 
Gene Names: pcaG
EC: 1.13.11.3
UniProt
Find proteins for P00436 (Pseudomonas putida)
Explore P00436 
Go to UniProtKB:  P00436
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protocatechuate 3,4-dioxygenase beta chainB, D, F, H, J, L238Pseudomonas putidaMutation(s): 2 
Gene Names: pcaH
EC: 1.13.11.3
UniProt
Find proteins for P00437 (Pseudomonas putida)
Explore P00437 
Go to UniProtKB:  P00437
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
B, D, F, H, J, LL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Binding Affinity Annotations 
IDSourceBinding Affinity
DHB Binding MOAD:  1YKP Kd: 1.10e+6 (nM) from 1 assay(s)
PDBBind:  1YKP Kd: 1.10e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.145 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 196.19α = 90
b = 127.97β = 97.68
c = 134.18γ = 90
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance