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Oxidoreductase PDB id
1dlq
Jmol
Contents
Protein chains
309 a.a. *
Ligands
LIO ×2
Metals
_FE ×2
_HG ×6
Waters ×125
* Residue conservation analysis
PDB id:
1dlq
Name: Oxidoreductase
Title: Structure of catechol 1,2-dioxygenase from acinetobacter sp. Inhibited by bound mercury
Structure: Catechol 1,2-dioxygenase. Chain: a, b. Synonym: 1,2-ctd. Engineered: yes
Source: Acinetobacter sp.. Organism_taxid: 62977. Strain: adp1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.188     R-free:   0.224
Authors: M.W.Vetting,D.H.Ohlendorf
Key ref:
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. PubMed id: 10801478 DOI: 10.1016/S0969-2126(00)00122-2
Date:
11-Dec-99     Release date:   23-May-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P07773  (CATA_ACIAD) -  Catechol 1,2-dioxygenase
Seq:
Struc: 		311 a.a.
309 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.13.11.1  - Catechol 1,2-dioxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Benzoate Metabolism
      Reaction: Catechol + O2 = cis,cis-muconate
Catechol
 + O(2)
 = cis,cis-muconate
      Cofactor: Iron
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cellular_component   1 term 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(00)00122-2 Structure 8:429-440 (2000)
PubMed id: 10801478  
 
 
The 1.8 A crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker.
M.W.Vetting, D.H.Ohlendorf.
 
  ABSTRACT  
 
BACKGROUND: Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. Catechol 1,2-dioxygenases (1, 2-CTDs) have a rudimentary design structure - a homodimer with one catalytic non-heme ferric ion per monomer, that is (alphaFe(3+))(2). This is in contrast to the archetypical intradiol dioxygenase protocatechuate 3,4-dioxygenase (3,4-PCD), which forms more diverse oligomers, such as (alphabetaFe(3+))(2-12). RESULTS: The crystal structure of 1,2-CTD from Acinetobacter sp. ADP1 (Ac 1,2-CTD) was solved by single isomorphous replacement and refined to 2.0 A resolution. The structures of the enzyme complexed with catechol and 4-methylcatechol were also determined at resolutions of 1.9 A and 1.8 A, respectively. While the characteristics of the iron ligands are similar, Ac 1,2-CTD differs from 3,4-PCDs in that only one subunit is used to fashion each active-site cavity. In addition, a novel 'helical zipper', consisting of five N-terminal helices from each subunit, forms the molecular dimer axis. Two phospholipids were unexpectedly found to bind within an 8 x 35 A hydrophobic tunnel along this axis. CONCLUSIONS: The helical zipper domain of Ac 1, 2-CTD has no equivalent in other proteins of known structure. Sequence analysis suggests the domain is a common motif in all members of the 1,2-CTD family. Complexes with catechol and 4-methylcatechol are the highest resolution complex structures to date of an intradiol dioxygenase. Furthermore, they confirm several observations seen in 3,4-PCDs, including ligand displacement upon binding exogenous ligands. The structures presented here are the first of a new family of intradiol dioxygenases.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. 2F[o]-F[c] electron density for the native and the two complexes around the active site. The electron density is contoured at 1s. (a) Ac 1,2-CTD with no substrate bound. (b) Ac 1,2-CTD soaked with 30 mM catechol. (c) Ac 1,2-CTD soaked with 30 mM 4-methylcatechol. (d,e,f) Same conditions as (a,b,c) only the model is rotated 90° around the horizontal axis. The figure was prepared with the molecular graphics program O [64].
 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 429-440) copyright 2000.  
  Figure was selected by an automated process.  

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.  
19672496 G.Di Nardo, C.Roggero, S.Campolongo, F.Valetti, F.Trotta, and G.Gilardi (2009).
Catalytic properties of catechol 1,2-dioxygenase from Acinetobacter radioresistens S13 immobilized on nanosponges.
  Dalton Trans, 0, 6507-6512.  
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.  
19300822 M.Brivio, J.Schlosrich, M.Ahmad, C.Tolond, and T.D.Bugg (2009).
Investigation of acid-base catalysis in the extradiol and intradiol catechol dioxygenase reactions using a broad specificity mutant enzyme and model chemistry.
  Org Biomol Chem, 7, 1368-1373.  
19301316 R.Caglio, F.Valetti, P.Caposio, G.Gribaudo, E.Pessione, and C.Giunta (2009).
Fine-tuning of catalytic properties of catechol 1,2-dioxygenase by active site tailoring.
  Chembiochem, 10, 1015-1024.  
17158677 M.Yoshida, T.Oikawa, H.Obata, K.Abe, H.Mihara, and N.Esaki (2007).
Biochemical and genetic analysis of the gamma-resorcylate (2,6-dihydroxybenzoate) catabolic pathway in Rhizobium sp. strain MTP-10005: identification and functional analysis of its gene cluster.
  J Bacteriol, 189, 1573-1581.  
17089147 S.C.Tsai, and Y.K.Li (2007).
Purification and characterization of a catechol 1,2-dioxygenase from a phenol degrading Candida albicans TL3.
  Arch Microbiol, 187, 199-206.  
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.  
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
15592943 O.Hayaishi (2005).
"Fifty years of oxygen activation".
  J Biol Inorg Chem, 10, 1-2.  
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.  
15689112 G.Di Nardo, E.Pessione, M.Cavaletto, L.Anfossi, A.Vanni, F.Briganti, and C.Giunta (2004).
Effects of surface hydrophobicity on the catalytic iron ion retention in the active site of two catechol 1,2-dioxygenase isoenzymes.
  Biometals, 17, 699-706.  
  12039004 M.J.Ryle, and R.P.Hausinger (2002).
Non-heme iron oxygenases.
  Curr Opin Chem Biol, 6, 193-201.  
12218013 O.V.Moiseeva, I.P.Solyanikova, S.R.Kaschabek, J.Gröning, M.Thiel, L.A.Golovleva, and M.Schlömann (2002).
A new modified ortho cleavage pathway of 3-chlorocatechol degradation by Rhodococcus opacus 1CP: genetic and biochemical evidence.
  J Bacteriol, 184, 5282-5292.  
11682193 C.H.Chua, Y.Feng, C.C.Yeo, H.E.Khoo, and C.L.Poh (2001).
Identification of amino acid residues essential for catalytic activity of gentisate 1,2-dioxygenase from Pseudomonas alcaligenes NCIB 9867.
  FEMS Microbiol Lett, 204, 141-146.  
11166568 P.K.Fyfe, K.E.McAuley, A.W.Roszak, N.W.Isaacs, R.J.Cogdell, and M.R.Jones (2001).
Probing the interface between membrane proteins and membrane lipids by X-ray crystallography.
  Trends Biochem Sci, 26, 106-112.  
  11578928 T.D.Bugg (2001).
Oxygenases: mechanisms and structural motifs for O(2) activation.
  Curr Opin Chem Biol, 5, 550-555.  
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.