PDBsum entry 1eo9

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
Jmol PyMol
Protein chains
202 a.a. *
238 a.a. *
Waters ×178
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure of acinetobacter sp. Adp1 protocatechuate dioxygenase at ph < 7.0
Structure: Protocatechuate 3,4-dioxygenase alpha chain. Chain: a. Engineered: yes. Protocatechuate 3,4-dioxygenase beta chain. Chain: b. Engineered: yes
Source: Acinetobacter sp.. Organism_taxid: 62977. Strain: adp1. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: 24mer (from PDB file)
2.00Å     R-factor:   0.179     R-free:   0.210
Authors: M.W.Vetting,D.A.D'Argenio,L.N.Ornston,D.H.Ohlendorf
Key ref:
M.W.Vetting et al. (2000). Structure of Acinetobacter strain ADP1 protocatechuate 3, 4-dioxygenase at 2.2 A resolution: implications for the mechanism of an intradiol dioxygenase. Biochemistry, 39, 7943-7955. PubMed id: 10891075 DOI: 10.1021/bi000151e
22-Mar-00     Release date:   09-Aug-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P20371  (PCXA_ACIAD) -  Protocatechuate 3,4-dioxygenase alpha chain
209 a.a.
202 a.a.*
Protein chain
Pfam   ArchSchema ?
P20372  (PCXB_ACIAD) -  Protocatechuate 3,4-dioxygenase beta chain
241 a.a.
238 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.  - Protocatechuate 3,4-dioxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Benzoate Metabolism
      Reaction: 3,4-dihydroxybenzoate + O2 = 3-carboxy-cis,cis-muconate
+ O(2)
= 3-carboxy-cis,cis-muconate
      Cofactor: Fe cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     catalytic activity     9 terms  


DOI no: 10.1021/bi000151e Biochemistry 39:7943-7955 (2000)
PubMed id: 10891075  
Structure of Acinetobacter strain ADP1 protocatechuate 3, 4-dioxygenase at 2.2 A resolution: implications for the mechanism of an intradiol dioxygenase.
M.W.Vetting, D.A.D'Argenio, L.N.Ornston, D.H.Ohlendorf.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21221570 A.Gosling, S.J.Fowler, M.S.O'Shea, M.Straffon, G.Dumsday, and M.Zachariou (2011).
Metabolic production of a novel polymer feedstock, 3-carboxy muconate, from vanillin.
  Appl Microbiol Biotechnol, 90, 107-116.  
21246129 N.Anitha, and M.Palaniandavar (2011).
Mononuclear iron(III) complexes of 3N ligands in organized assemblies: spectral and redox properties and attainment of regioselective extradiol dioxygenase activity.
  Dalton Trans, 40, 1888-1901.  
20835480 R.Mayilmurugan, M.Sankaralingam, E.Suresh, and M.Palaniandavar (2010).
Novel square pyramidal iron(III) complexes of linear tetradentate bis(phenolate) ligands as structural and reactive models for intradiol-cleaving 3,4-PCD enzymes: Quinone formation vs. intradiol cleavage.
  Dalton Trans, 39, 9611-9625.  
19574301 J.Deveryshetty, and P.S.Phale (2009).
Biodegradation of phenanthrene by Pseudomonas sp. strain PPD: purification and characterization of 1-hydroxy-2-naphthoic acid dioxygenase.
  Microbiology, 155, 3083-3091.  
19845332 L.H.Do, and S.J.Lippard (2009).
2-Phenoxypyridyl dinucleating ligands for assembly of diiron(II) complexes: efficient reactivity with O(2) to form (mu-Oxo)diiron(III) units.
  Inorg Chem, 48, 10708-10719.  
17213657 E.Masai, Y.Katayama, and M.Fukuda (2007).
Genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds.
  Biosci Biotechnol Biochem, 71, 1.  
17256852 M.Y.Pau, M.I.Davis, A.M.Orville, J.D.Lipscomb, and E.I.Solomon (2007).
Spectroscopic and electronic structure study of the enzyme-substrate complex of intradiol dioxygenases: substrate activation by a high-spin ferric non-heme iron site.
  J Am Chem Soc, 129, 1944-1958.  
15722436 A.P.Citadini, A.P.Pinto, A.P.Araújo, O.R.Nascimento, and A.J.Costa-Filho (2005).
EPR studies of chlorocatechol 1,2-dioxygenase: evidences of iron reduction during catalysis and of the binding of amphipatic molecules.
  Biophys J, 88, 3502-3508.  
16153178 D.M.Young, D.Parke, and L.N.Ornston (2005).
Opportunities for genetic investigation afforded by Acinetobacter baylyi, a nutritionally versatile bacterial species that is highly competent for natural transformation.
  Annu Rev Microbiol, 59, 519-551.  
15772073 M.Ferraroni, J.Seifert, V.M.Travkin, M.Thiel, S.Kaschabek, A.Scozzafava, L.Golovleva, M.Schlömann, and F.Briganti (2005).
Crystal structure of the hydroxyquinol 1,2-dioxygenase from Nocardioides simplex 3E, a key enzyme involved in polychlorinated aromatics biodegradation.
  J Biol Chem, 280, 21144-21154.
PDB code: 1tmx
16317455 M.L.Neidig, and E.I.Solomon (2005).
Structure-function correlations in oxygen activating non-heme iron enzymes.
  Chem Commun (Camb), (), 5843-5863.  
16329976 M.T.García, A.Ventosa, and E.Mellado (2005).
Catabolic versatility of aromatic compound-degrading halophilic bacteria.
  FEMS Microbiol Ecol, 54, 97.  
16030237 S.Liu, N.Ogawa, T.Senda, A.Hasebe, and K.Miyashita (2005).
Amino acids in positions 48, 52, and 73 differentiate the substrate specificities of the highly homologous chlorocatechol 1,2-dioxygenases CbnA and TcbC.
  J Bacteriol, 187, 5427-5436.  
15006791 A.Buchan, E.L.Neidle, and M.A.Moran (2004).
Diverse organization of genes of the beta-ketoadipate pathway in members of the marine Roseobacter lineage.
  Appl Environ Microbiol, 70, 1658-1668.  
15487948 C.K.Brown, M.W.Vetting, C.A.Earhart, and D.H.Ohlendorf (2004).
Biophysical analyses of designed and selected mutants of protocatechuate 3,4-dioxygenase1.
  Annu Rev Microbiol, 58, 555-585.
PDB codes: 2bum 2buq 2bur 2but 2buv
14993710 E.Skrzypczak-Jankun, O.Y.Borbulevych, and J.Jankun (2004).
Soybean lipoxygenase-3 in complex with 4-nitrocatechol.
  Acta Crystallogr D Biol Crystallogr, 60, 613-615.
PDB code: 1no3
15060064 M.Ferraroni, I.P.Solyanikova, M.P.Kolomytseva, A.Scozzafava, L.Golovleva, and F.Briganti (2004).
Crystal structure of 4-chlorocatechol 1,2-dioxygenase from the chlorophenol-utilizing gram-positive Rhodococcus opacus 1CP.
  J Biol Chem, 279, 27646-27655.
PDB code: 1s9a
12957923 X.Y.Zhu, J.Lubeck, and J.J.Kilbane (2003).
Characterization of microbial communities in gas industry pipelines.
  Appl Environ Microbiol, 69, 5354-5363.  
12037322 M.Ferraroni, M.Y.Ruiz Tarifa, F.Briganti, A.Scozzafava, S.Mangani, I.P.Solyanikova, M.P.Kolomytseva, and L.Golovleva (2002).
4-Chlorocatechol 1,2-dioxygenase from the chlorophenol-utilizing Gram-positive Rhodococcus opacus 1CP: crystallization and preliminary crystallographic analysis.
  Acta Crystallogr D Biol Crystallogr, 58, 1074-1076.  
12039004 M.J.Ryle, and R.P.Hausinger (2002).
Non-heme iron oxygenases.
  Curr Opin Chem Biol, 6, 193-201.  
11722937 A.Buchan, E.L.Neidle, and M.A.Moran (2001).
Diversity of the ring-cleaving dioxygenase gene pcaH in a salt marsh bacterial community.
  Appl Environ Microbiol, 67, 5801-5809.  
11445161 D.A.D'Argenio, A.Segura, P.V.Bünz, and L.N.Ornston (2001).
Spontaneous mutations affecting transcriptional regulation by protocatechuate in Acinetobacter.
  FEMS Microbiol Lett, 201, 15-19.  
11454212 M.Contzen, S.Bürger, and A.Stolz (2001).
Cloning of the genes for a 4-sulphocatechol-oxidizing protocatechuate 3,4-dioxygenase from Hydrogenophaga intermedia S1 and identification of the amino acid residues responsible for the ability to convert 4-sulphocatechol.
  Mol Microbiol, 41, 199-205.  
11055908 A.Buchan, L.S.Collier, E.L.Neidle, and M.A.Moran (2000).
Key aromatic-ring-cleaving enzyme, protocatechuate 3,4-dioxygenase, in the ecologically important marine Roseobacter lineage.
  Appl Environ Microbiol, 66, 4662-4672.  
11029436 D.Parke (2000).
Positive selection for mutations affecting bioconversion of aromatic compounds in Agrobacterium tumefaciens: analysis of spontaneous mutations in the protocatechuate 3,4-dioxygenase gene.
  J Bacteriol, 182, 6145-6153.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.