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PDBsum entry 3pcn

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protein ligands metals Protein-protein interface(s) links
Dioxygenase PDB id
3pcn
Jmol
Contents
Protein chains
(+ 0 more) 200 a.a. *
(+ 0 more) 233 a.a. *
Ligands
BME ×6
DHY ×6
Metals
_FE ×6
Waters ×1374
* Residue conservation analysis
PDB id:
3pcn
Name: Dioxygenase
Title: Structure of protocatechuate 3,4-dioxygenase complexed with dihydroxyphenylacetate
Structure: Protocatechuate 3,4-dioxygenase. Chain: a, b, c, d, e, f. Other_details: entry contains alpha/beta 6-mer. Protocatechuate 3,4-dioxygenase. Chain: m, n, o, p, q, r. Other_details: entry contains alpha/beta 6-mer
Source: Pseudomonas putida. Organism_taxid: 303. Atcc: 23975. Other_details: previously classified as pseudomonas aerugin
Biol. unit: 24mer (from PDB file)
Resolution:
2.40Å     R-factor:   0.166    
Authors: A.M.Orville,J.D.Lipscomb,D.H.Ohlendorf
Key ref:
T.E.Elgren et al. (1997). Crystal structure and resonance Raman studies of protocatechuate 3,4-dioxygenase complexed with 3,4-dihydroxyphenylacetate. Biochemistry, 36, 11504-11513. PubMed id: 9298971 DOI: 10.1021/bi970691k
Date:
19-Aug-97     Release date:   25-Feb-98    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00436  (PCXA_PSEPU) -  Protocatechuate 3,4-dioxygenase alpha chain
Seq:
Struc:
201 a.a.
200 a.a.
Protein chains
Pfam   ArchSchema ?
P00437  (PCXB_PSEPU) -  Protocatechuate 3,4-dioxygenase beta chain
Seq:
Struc:
239 a.a.
233 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, M, B, N, C, O, D, P, E, Q, F, R: E.C.1.13.11.3  - Protocatechuate 3,4-dioxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Benzoate Metabolism
      Reaction: 3,4-dihydroxybenzoate + O2 = 3-carboxy-cis,cis-muconate
3,4-dihydroxybenzoate
Bound ligand (Het Group name = DHY)
matches with 91.67% similarity
+ 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     8 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi970691k Biochemistry 36:11504-11513 (1997)
PubMed id: 9298971  
 
 
Crystal structure and resonance Raman studies of protocatechuate 3,4-dioxygenase complexed with 3,4-dihydroxyphenylacetate.
T.E.Elgren, A.M.Orville, K.A.Kelly, J.D.Lipscomb, D.H.Ohlendorf, L.Que.
 
  ABSTRACT  
 
The crystal structure of the anaerobic complex of Pseudomonas putida protocatechuate 3,4-dioxygenase (3,4-PCD) bound with the alternative substrate, 3,4-dihydroxyphenylacetate (HPCA), is reported at 2.4 A resolution and refined to an R factor of 0.17. Formation of the active site Fe(III).HPCA chelated complex causes the endogenous axial tyrosinate, Tyr447 (147beta), to dissociate from the iron and rotate into an alternative orientation analogous to that previously observed in the anaerobic 3,4-PCD.3,4-dihydroxybenzoate complex (3, 4-PCD.PCA) [Orville, A. M., Lipscomb, J. D., & Ohlendorf, D. H. (1997) Biochemistry 36, 10052-10066]. Two orientations of the aromatic ring of HPCA related by an approximate 180 degrees rotation within the active site are consistent with the electron density. Resonance Raman (rR) spectroscopic data from Brevibacteriumfuscum 3,4-PCD.HPCA complex in solution reveals low frequency rR vibrational bands between 500 and 650 cm-1 as well as a band at approximately 1320 cm-1 which are diagnostic of a HPCA. Fe(III) chelate complex. 18O labeling of HPCA at either the C4 or C3 hydroxyl group unambiguously establishes the vibrational coupling modes associated with the five-membered chelate ring system. Analysis of these data suggests that the Fe(III)-HPCAO4 bond is shorter than the Fe(III)-HPCAO3 bond. This consequently favors the model for the crystal structure in which the C3 phenolic function occupies the Fe3+ ligand site opposite the endogenous ligand Tyr408(Oeta) (108beta). This is essentially the same binding orientation as proposed for PCA in the crystal structure of the anaerobic 3,4-PCD.PCA complex based solely on direct modeling of the 2Fo - Fc electron density and suggests that this is the conformation required for catalysis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
20059399 L.M.Blank, B.E.Ebert, K.Buehler, and B.Bühler (2010).
Redox biocatalysis and metabolism: molecular mechanisms and metabolic network analysis.
  Antioxid Redox Signal, 13, 349-394.  
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.  
17334823 K.H.Kim (2007).
Outliers in SAR and QSAR: is unusual binding mode a possible source of outliers?
  J Comput Aided Mol Des, 21, 63-86.  
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.  
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.  
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
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
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.  
10607676 C.J.Schofield, and Z.Zhang (1999).
Structural and mechanistic studies on 2-oxoglutarate-dependent oxygenases and related enzymes.
  Curr Opin Struct Biol, 9, 722-731.  
10467151 K.Sugimoto, T.Senda, H.Aoshima, E.Masai, M.Fukuda, and Y.Mitsui (1999).
Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions.
  Structure, 7, 953-965.
PDB codes: 1b4u 1bou
10089329 M.Benvenuti, F.Briganti, A.Scozzafava, L.Golovleva, V.M.Travkin, and S.Mangani (1999).
Crystallization and preliminary crystallographic analysis of the hydroxyquinol 1,2-dioxygenase from Nocardioides simplex 3E: a novel dioxygenase involved in the biodegradation of polychlorinated aromatic compounds.
  Acta Crystallogr D Biol Crystallogr, 55, 901-903.  
9857017 F.H.Vaillancourt, S.Han, P.D.Fortin, J.T.Bolin, and L.D.Eltis (1998).
Molecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol.
  J Biol Chem, 273, 34887-34895.
PDB codes: 1kmy 1knd 1knf
9485360 R.W.Frazee, A.M.Orville, K.B.Dolbeare, H.Yu, D.H.Ohlendorf, and J.D.Lipscomb (1998).
The axial tyrosinate Fe3+ ligand in protocatechuate 3,4-dioxygenase influences substrate binding and product release: evidence for new reaction cycle intermediates.
  Biochemistry, 37, 2131-2144.
PDB code: 3pcd
9667935 S.J.Lange, and L.Que (1998).
Oxygen activating nonheme iron enzymes.
  Curr Opin Chem Biol, 2, 159-172.  
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.