1EOC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

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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

  • DOI: 10.1021/bi000151e
  • Primary Citation of Related Structures:  
    1EO2, 1EO9, 1EOB, 1EOA, 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 3, 4-dihydroxybenzoic acid (PCA), the inhibitor 4-nitrocatechol (4-NC), or cyanide (CN(-)) have been solved using native phases ...

    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: 
    • 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
    • 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
    • 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
    • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAINA209Acinetobacter baylyi ADP1Mutation(s): 0 
Gene Names: pcaGACIAD1712
EC: 1.13.11.3
UniProt
Find proteins for P20371 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1))
Explore P20371 
Go to UniProtKB:  P20371
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAINB241Acinetobacter baylyi ADP1Mutation(s): 0 
Gene Names: pcaHACIAD1711
EC: 1.13.11.3
UniProt
Find proteins for P20372 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1))
Explore P20372 
Go to UniProtKB:  P20372
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4NC (Subject of Investigation/LOI)
Query on 4NC

Download Ideal Coordinates CCD File 
D [auth B]4-NITROCATECHOL
C6 H5 N O4
XJNPNXSISMKQEX-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
C [auth B]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
4NC Binding MOAD:  1EOC Ki: 900 (nM) from 1 assay(s)
PDBBind:  1EOC Ki: 900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.3α = 90
b = 144.3β = 90
c = 144.3γ = 90
Software Package:
Software NamePurpose
CNSrefinement
X-GENdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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