PDBsum entry 3pcm

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protein ligands metals Protein-protein interface(s) links
Dioxygenase PDB id
Jmol PyMol
Protein chains
(+ 0 more) 200 a.a. *
(+ 0 more) 233 a.a. *
CYN ×6
NNO ×6
_FE ×6
Waters ×1416
* Residue conservation analysis
PDB id:
Name: Dioxygenase
Title: Structure of protocatechuate 3,4-dioxygenase complexed with hydroxynicotinic acid n-oxide and cyanide
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)
2.25Å     R-factor:   0.180    
Authors: A.M.Orville,J.D.Lipscomb,D.H.Ohlendorf
Key ref:
A.M.Orville et al. (1997). Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: endogenous Fe3+ ligand displacement in response to substrate binding. Biochemistry, 36, 10052-10066. PubMed id: 9254600 DOI: 10.1021/bi970469f
18-Jul-97     Release date:   21-Jan-98    
Go to PROCHECK summary

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

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

Benzoate Metabolism
      Reaction: 3,4-dihydroxybenzoate + O2 = 3-carboxy-cis,cis-muconate
Bound ligand (Het Group name = NNO)
matches with 69.23% 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  


DOI no: 10.1021/bi970469f Biochemistry 36:10052-10066 (1997)
PubMed id: 9254600  
Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: endogenous Fe3+ ligand displacement in response to substrate binding.
A.M.Orville, J.D.Lipscomb, D.H.Ohlendorf.
Protocatechuate 3,4-dioxygenase (3,4-PCD) utilizes a ferric ion to catalyze the aromatic ring cleavage of 3,4-dihydroxybenzoate (PCA) by incorporation of both atoms of dioxygen to yield beta-carboxy-cis, cis-muconate. The crystal structures of the anaerobic 3,4-PCD.PCA complex, aerobic complexes with two heterocyclic PCA analogs, 2-hydroxyisonicotinic acid N-oxide (INO) and 6-hydroxynicotinic acid N-oxide (NNO), and ternary complexes of 3,4-PCD.INO.CN and 3,4-PCD. NNO.CN have been determined at 2.1-2.2 A resolution and refined to R-factors between 0.165 and 0.184. PCA, INO, and NNO form very similar, asymmetrically chelated complexes with the active site Fe3+ that result in dissociation of the endogenous axial tyrosinate Fe3+ ligand, Tyr447 (147beta). After its release from the iron, Tyr447 is stabilized by hydrogen bonding to Tyr16 (16alpha) and Asp413 (113beta) and forms the top of a small cavity adjacent to the C3-C4 bond of PCA. The equatorial Fe3+ coordination site within this cavity is unoccupied in the anaerobic 3,4-PCD.PCA complex but coordinates a solvent molecule in the 3,4-PCD.INO and 3,4-PCD.NNO complexes and CN- in the 3,4-PCD.INO.CN and 3,4-PCD.NNO.CN complexes. This shows that an O2 analog can occupy the cavity and suggests that electrophilic O2 attack on PCA is initiated from this site. Both the dissociation of the endogenous Tyr447 and the expansion of the iron coordination sphere are novel features of the 3,4-PCD. substrate complex which appear to play essential roles in the activation of substrate for O2 attack. Together, the structures presented here and in the preceding paper [Orville, A. M., Elango, N. , Lipscomb, J. D., & Ohlendorf, D. H. (1997) Biochemistry 36, 10039-10051] provide atomic models for several steps in the reaction cycle of 3,4-PCD and related Fe3+-containing dioxygenases.

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.  
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.  
18226222 R.An, S.Sreevatsan, and P.S.Grewal (2008).
Moraxella osloensis gene expression in the slug host Deroceras reticulatum.
  BMC Microbiol, 8, 19.  
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.  
18003930 M.Y.Pau, J.D.Lipscomb, and E.I.Solomon (2007).
Substrate activation for O2 reactions by oxidized metal centers in biology.
  Proc Natl Acad Sci U S A, 104, 18355-18362.  
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.  
17427160 N.El Azhari, S.Chabaud, A.Percept, D.Bru, and F.Martin-Laurent (2007).
pcaH, a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in the soil environment.
  Pest Manag Sci, 63, 459-467.  
16936929 I.A.Koval, P.Gamez, C.Belle, K.Selmeczi, and J.Reedijk (2006).
Synthetic models of the active site of catechol oxidase: mechanistic studies.
  Chem Soc Rev, 35, 814-840.  
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.  
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
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
15028678 M.W.Vetting, L.P.Wackett, L.Que, J.D.Lipscomb, and D.H.Ohlendorf (2004).
Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases.
  J Bacteriol, 186, 1945-1958.
PDB codes: 1f1r 1f1u 1f1v 1f1x 1q0c 1q0o
12598659 E.I.Solomon, A.Decker, and N.Lehnert (2003).
Non-heme iron enzymes: contrasts to heme catalysis.
  Proc Natl Acad Sci U S A, 100, 3589-3594.  
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.  
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.  
11578928 T.D.Bugg (2001).
Oxygenases: mechanisms and structural motifs for O(2) activation.
  Curr Opin Chem Biol, 5, 550-555.  
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.  
10736169 B.Schwartz, J.E.Dove, and J.P.Klinman (2000).
Kinetic analysis of oxygen utilization during cofactor biogenesis in a copper-containing amine oxidase from yeast.
  Biochemistry, 39, 3699-3707.  
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.  
10736168 J.E.Dove, B.Schwartz, N.K.Williams, and J.P.Klinman (2000).
Investigation of spectroscopic intermediates during copper-binding and TPQ formation in wild-type and active-site mutants of a copper-containing amine oxidase from yeast.
  Biochemistry, 39, 3690-3698.  
11029433 M.Contzen, and A.Stolz (2000).
Characterization of the genes for two protocatechuate 3, 4-dioxygenases from the 4-sulfocatechol-degrading bacterium Agrobacterium radiobacter strain S2.
  J Bacteriol, 182, 6123-6129.  
10891075 M.W.Vetting, D.A.D'Argenio, L.N.Ornston, and D.H.Ohlendorf (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.
PDB codes: 1eo2 1eo9 1eoa 1eob 1eoc
10801478 M.W.Vetting, and D.H.Ohlendorf (2000).
The 1.8 A crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker.
  Structure, 8, 429-440.
PDB codes: 1dlm 1dlq 1dlt 1dmh
10742233 S.G.Iwagami, K.Yang, and J.Davies (2000).
Characterization of the protocatechuic acid catabolic gene cluster from Streptomyces sp. strain 2065.
  Appl Environ Microbiol, 66, 1499-1508.  
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.  
  10515940 D.A.D'Argenio, M.W.Vetting, D.H.Ohlendorf, and L.N.Ornston (1999).
Substitution, insertion, deletion, suppression, and altered substrate specificity in functional protocatechuate 3,4-dioxygenases.
  J Bacteriol, 181, 6478-6487.  
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.  
10194363 S.K.Lee, and J.D.Lipscomb (1999).
Oxygen activation catalyzed by methane monooxygenase hydroxylase component: proton delivery during the O-O bond cleavage steps.
  Biochemistry, 38, 4423-4432.  
9667942 A.J.Thomson, and H.B.Gray (1998).
Bio-inorganic chemistry
  Curr Opin Chem Biol, 2, 155-158.  
9622501 M.Merkx, and B.A.Averill (1998).
Ga3+ as a functional substitute for Fe3+: preparation and characterization of the Ga3+Fe2+ and Ga3+Zn2+ forms of bovine spleen purple acid phosphatase.
  Biochemistry, 37, 8490-8497.  
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.  
9369476 A.M.Orville, and J.D.Lipscomb (1997).
Cyanide and nitric oxide binding to reduced protocatechuate 3,4-dioxygenase: insight into the basis for order-dependent ligand binding by intradiol catecholic dioxygenases.
  Biochemistry, 36, 14044-14055.  
9254599 A.M.Orville, N.Elango, J.D.Lipscomb, and D.H.Ohlendorf (1997).
Structures of competitive inhibitor complexes of protocatechuate 3,4-dioxygenase: multiple exogenous ligand binding orientations within the active site.
  Biochemistry, 36, 10039-10051.
PDB codes: 3pcb 3pcc 3pce 3pcf 3pcg 3pch 3pci
9298971 T.E.Elgren, A.M.Orville, K.A.Kelly, J.D.Lipscomb, D.H.Ohlendorf, and L.Que (1997).
Crystal structure and resonance Raman studies of protocatechuate 3,4-dioxygenase complexed with 3,4-dihydroxyphenylacetate.
  Biochemistry, 36, 11504-11513.
PDB code: 3pcn
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.