1EOA

CRYSTAL STRUCTURE OF ACINETOBACTER SP. ADP1 PROTOCATECHUATE 3,4-DIOXYGENASE IN COMPLEX WITH CYANIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of Acinetobacter strain ADP1 protocatechuate 3, 4-dioxygenase at 2.2 A resolution: implications for the mechanism of an intradiol dioxygenase.

Vetting, M.W.D'Argenio, D.A.Ornston, L.N.Ohlendorf, D.H.

(2000) Biochemistry 39: 7943-7955

  • Primary Citation of Related Structures:  1EO2, 1EO9, 1EOB, 1EOC

  • PubMed Abstract: 
  • The crystal structures of protocatechuate 3,4-dioxygenase from the soil bacteria Acinetobacterstrain ADP1 (Ac 3,4-PCD) have been determined in space group I23 at pH 8.5 and 5.75. In addition, the structures of Ac 3,4-PCD complexed with its substrate ...

    The crystal structures of protocatechuate 3,4-dioxygenase from the soil bacteria Acinetobacterstrain ADP1 (Ac 3,4-PCD) have been determined in space group I23 at pH 8.5 and 5.75. In addition, the structures of Ac 3,4-PCD complexed with its substrate 3, 4-dihydroxybenzoic acid (PCA), the inhibitor 4-nitrocatechol (4-NC), or cyanide (CN(-)) have been solved using native phases. The overall tertiary and quaternary structures of Ac 3,4-PCD are similar to those of the same enzyme from Pseudomonas putida[Ohlendorf et al. (1994) J. Mol. Biol. 244, 586-608]. At pH 8.5, the catalytic non-heme Fe(3+) is coordinated by two axial ligands, Tyr447(OH) (147beta) and His460(N)(epsilon)(2) (160beta), and three equatorial ligands, Tyr408(OH) (108beta), His462(N)(epsilon)(2) (162beta), and a hydroxide ion (d(Fe-OH) = 1.91 A) in a distorted bipyramidal geometry. At pH 5.75, difference maps suggest a sulfate binds to the Fe(3+) in an equatorial position and the hydroxide is shifted [d(Fe-OH) = 2.3 A] yielding octahedral geometry for the active site Fe(3+). This change in ligation geometry is concomitant with a shift in the optical absorbance spectrum of the enzyme from lambda(max) = 450 nm to lambda(max) = 520 nm. Binding of substrate or 4-NC to the Fe(3+) is bidentate with the axial ligand Tyr447(OH) (147beta) dissociating. The structure of the 4-NC complex supports the view that resonance delocalization of the positive character of the nitrogen prevents substrate activation. The cyanide complex confirms previous work that protocatechuate 3,4-dioxygenases have three coordination sites available for binding by exogenous substrates. A significant conformational change extending away from the active site is seen in all structures when compared to the native enzyme at pH 8.5. This conformational change is discussed in its relevance to enhancing catalysis in protocatechuate 3,4-dioxygenases.


    Related Citations: 
    • Crystal Structures of Substrate and Substrate Analog Complexes of Protocatechuate 3,4-dioxygenase: Endogenous Fe3+ Ligand Displacement in Response to Substrate binding.
      Orville, A.M.,Lipscomb, J.D.,Ohlendorf, D.H.
      (1997) Biochemistry 36: 10052
    • Substitution, Insertion, Deletion, Suppression, and Altered Substrate Specificity in Functional Protocatechuate 3,4-dioxygenases.
      D'Argenio, D.A.,Vetting, M.W.,Ohlendorf, D.H.,Ornston, L.N.
      (1999) J.Bacteriol. 181: 6478
    • Crystallization and Preliminary X-ray Analysis of Protocatechuate 3,4-dioxygenase from Acinetobacter calcoaceticus
      Vetting, M.W.,Earhart, C.A.,Ohlendorf, D.H.
      (1994) J.Mol.Biol. 236: 372
    • 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


    Organizational Affiliation

    Center of Metals in Biocatalysis and Department of Biochemistry, Molecular Biology and Biophysics, 6-155 Jackson Hall, 321 Church St. S.E., University of Minnesota Medical School, Minneapolis, Minnesota 55455-0347, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN
A
209Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)Gene Names: pcaG
EC: 1.13.11.3
Find proteins for P20371 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1))
Go to UniProtKB:  P20371
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN
B
241Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)Gene Names: pcaH
EC: 1.13.11.3
Find proteins for P20372 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1))
Go to UniProtKB:  P20372
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYN
Query on CYN

Download SDF File 
Download CCD File 
B
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.186 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 144.900α = 90.00
b = 144.900β = 90.00
c = 144.900γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
X-GENdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-08-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description