3PCC

STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 4-HYDROXYBENZOATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structures of competitive inhibitor complexes of protocatechuate 3,4-dioxygenase: multiple exogenous ligand binding orientations within the active site.

Orville, A.M.Elango, N.Lipscomb, J.D.Ohlendorf, D.H.

(1997) Biochemistry 36: 10039-10051

  • DOI: 10.1021/bi970468n
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protocatechuate 3,4-dioxygenase (3,4-PCD) catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis, cis-muconate. Crystal structures of Pseudomonas putida3,4-PCD [quaternary structure of (alphabetaFe3+)12] complexed ...

    Protocatechuate 3,4-dioxygenase (3,4-PCD) catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis, cis-muconate. Crystal structures of Pseudomonas putida3,4-PCD [quaternary structure of (alphabetaFe3+)12] complexed with seven competitive inhibitors [3-hydroxyphenylacetate (MHP), 4-hydroxyphenylacetate (PHP), 3-hydroxybenzoate (MHB), 4-hydroxybenzoate (PHB), 3-fluoro-4-hydroxybenzoate (FHB), 3-chloro-4-hydroxybenzoate (CHB), and 3-iodo-4-hydroxybenzoate (IHB)] are reported at 2.0-2.2 A resolution with R-factors of 0. 0.159-0.179. The inhibitors bind in a narrow active site crevasse lined with residues that provide a microenvironment that closely matches the chemical characteristics of the inhibitors. This results in as little as 20% solvent-exposed surface area for the higher-affinity inhibitors (PHB, CHB, and FHB). In uncomplexed 3,4-PCD, the active site Fe3+ is bound at the bottom of the active site crevasse by four endogenous ligands and a solvent molecule (Wat827). The orientations of the endogenous ligands are relatively unperturbed in each inhibitor complex, but the inhibitors themselves bind to or near the iron in a range of positions, all of which perturb the position of Wat827. The three lowest-affinity inhibitors (MHP, PHP, and IHB) yield distorted trigonal bipyramidal iron coordination geometry in which the inhibitor C4-phenolate group displaces the solvent ligand. MHB binds within the active site, but neither its C3-OH group nor the solvent molecule binds to the iron. The C4-phenolate group of the three highest-affinity inhibitors (PHB, CHB, and FHB) coordinates the Fe3+ adjacent to Wat827, resulting in a shift in its position to yield a six-coordinate distorted octahedral geometry. The range of inhibitor orientations may mimic the mechanistically significant stages of substrate binding to 3, 4-PCD. The structure of the final substrate complex is reported in the following paper [Orville, A. M., Lipscomb, J. D., & Ohlendorf, D. H. (1997) Biochemistry 36, 10052-10066].


    Related Citations: 
    • Determination of the Quaternary Structure of Protocatechuate 3,4-Dioxygenase from Pseudomonas Aeruginosa
      Ohlendorf, D.H.,Weber, P.C.,Lipscomb, J.D.
      (1987) J.Mol.Biol. 195: 225
    • Structure of Protocatechuate 3,4-Dioxygenase from Pseudomonas Aeruginosa at 2.15 A Resolution
      Ohlendorf, D.H.,Orville, A.M.,Lipscomb, J.D.
      (1994) J.Mol.Biol. 244: 586
    • Structure and Assembly of Protocatechuate 3,4-Dioxygenase
      Ohlendorf, D.H.,Lipscomb, J.D.,Weber, P.C.
      (1988) Nature 336: 403


    Organizational Affiliation

    Department of Biochemistry, Medical School, and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455-0347, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTOCATECHUATE 3,4-DIOXYGENASE
A, B, C, D, E, F
200Pseudomonas putidaMutation(s): 0 
Gene Names: pcaG
EC: 1.13.11.3
Find proteins for P00436 (Pseudomonas putida)
Go to UniProtKB:  P00436
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTOCATECHUATE 3,4-DIOXYGENASE
M, N, O, P, Q, R
238Pseudomonas putidaMutation(s): 0 
Gene Names: pcaH
EC: 1.13.11.3
Find proteins for P00437 (Pseudomonas putida)
Go to UniProtKB:  P00437
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PHB
Query on PHB

Download SDF File 
Download CCD File 
M, N, O, P, Q, R
P-HYDROXYBENZOIC ACID
C7 H6 O3
FJKROLUGYXJWQN-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
M, N, O, P, Q, R
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
M, N, O, P, Q, R
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PHBKi: 240000 nM BINDINGMOAD
PHBKi: 240000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Work: 0.163 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 197.410α = 90.00
b = 127.970β = 97.80
c = 134.880γ = 90.00
Software Package:
Software NamePurpose
XENGENdata scaling
PROLSQrefinement
XENGENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-29
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other