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PDBsum entry 1mpy

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1mpy
Jmol
Contents
Protein chains
307 a.a. *
Ligands
ACN ×4
Metals
FE2 ×4
Waters ×112
* Residue conservation analysis
PDB id:
1mpy
Name: Oxidoreductase
Title: Structure of catechol 2,3-dioxygenase (metapyrocatechase) from pseudomonas putida mt-2
Structure: Catechol 2,3-dioxygenase. Chain: a, b, c, d. Synonym: metapyrocatechase, mpc. Engineered: yes. Other_details: fe(ii) form
Source: Pseudomonas putida. Organism_taxid: 303. Strain: mt-2. Atcc: atcc 23973. Collection: atcc 23973. Gene: xyle. Expressed in: escherichia coli str. K12 substr. W3110. Expression_system_taxid: 316407.
Biol. unit: Homo-Tetramer (from PDB file)
Resolution:
2.80Å     R-factor:   0.200     R-free:   0.280
Authors: A.Kita,S.Kita,I.Fujisawa,K.Inaka,T.Ishida,K.Horiike, M.Nozaki,K.Miki
Key ref:
A.Kita et al. (1999). An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Ppseudomonas putida mt-2. Structure, 7, 25-34. PubMed id: 10368270 DOI: 10.1016/S0969-2126(99)80006-9
Date:
20-Oct-98     Release date:   18-May-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P06622  (XYLE1_PSEPU) -  Metapyrocatechase
Seq:
Struc:
307 a.a.
307 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.13.11.2  - Catechol 2,3-dioxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Catechol + O2 = 2-hydroxymuconate-6-semialdehyde
Catechol
Bound ligand (Het Group name = ACN)
matches with 50.00% similarity
+ O(2)
= 2-hydroxymuconate-6-semialdehyde
      Cofactor: Fe(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/S0969-2126(99)80006-9 Structure 7:25-34 (1999)
PubMed id: 10368270  
 
 
An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Ppseudomonas putida mt-2.
A.Kita, S.Kita, I.Fujisawa, K.Inaka, T.Ishida, K.Horiike, M.Nozaki, K.Miki.
 
  ABSTRACT  
 
BACKGROUND: Catechol dioxygenases catalyze the ring cleavage of catechol and its derivatives in either an intradiol or extradiol manner. These enzymes have a key role in the degradation of aromatic molecules in the environment by soil bacteria. Catechol 2, 3-dioxygenase catalyzes the incorporation of dioxygen into catechol and the extradiol ring cleavage to form 2-hydroxymuconate semialdehyde. Catechol 2,3-dioxygenase (metapyrocatechase, MPC) from Pseudomonas putida mt-2 was the first extradiol dioxygenase to be obtained in a pure form and has been studied extensively. The lack of an MPC structure has hampered the understanding of the general mechanism of extradiol dioxygenases. RESULTS: The three-dimensional structure of MPC has been determined at 2.8 A resolution by the multiple isomorphous replacement method. The enzyme is a homotetramer with each subunit folded into two similar domains. The structure of the MPC subunit resembles that of 2,3-dihydroxybiphenyl 1,2-dioxygenase, although there is low amino acid sequence identity between these enzymes. The active-site structure reveals a distorted tetrahedral Fe(II) site with three endogenous ligands (His153, His214 and Glu265), and an additional molecule that is most probably acetone. CONCLUSIONS: The present structure of MPC, combined with those of two 2,3-dihydroxybiphenyl 1,2-dioxygenases, reveals a conserved core region of the active site comprising three Fe(II) ligands (His153, His214 and Glu265), one tyrosine (Tyr255) and two histidine (His199 and His246) residues. The results suggest that extradiol dioxygenases employ a common mechanism to recognize the catechol ring moiety of various substrates and to activate dioxygen. One of the conserved histidine residues (His199) seems to have important roles in the catalytic cycle.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Schematic drawing of the assembly features of the MPC molecule. Protein monomers are drawn in purple or green with the protruding loops colored in yellow. Fe atoms are shown as red spheres and the three residues liganded to the Fe(II) atom are shown as ball-and-stick models. (a) A side view of the whole tetramer. (b) A tentative dimer of MPC. The figures were created using the program MOLSCRIPT [34] and rendered with RASTER3D [35].
 
  The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 25-34) copyright 1999.  
  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.  
19688300 J.Wei, Y.Zhou, T.Xu, and B.Lu (2010).
Rational design of catechol-2, 3-dioxygenase for improving the enzyme characteristics.
  Appl Biochem Biotechnol, 162, 116-126.  
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.  
19828456 J.H.Cho, D.K.Jung, K.Lee, and S.Rhee (2009).
Crystal structure and functional analysis of the extradiol dioxygenase LapB from a long-chain alkylphenol degradation pathway in Pseudomonas.
  J Biol Chem, 284, 34321-34330.
PDB codes: 3hpv 3hpy 3hq0
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.  
18502868 M.J.Moonen, N.M.Kamerbeek, A.H.Westphal, S.A.Boeren, D.B.Janssen, M.W.Fraaije, and W.J.van Berkel (2008).
Elucidation of the 4-hydroxyacetophenone catabolic pathway in Pseudomonas fluorescens ACB.
  J Bacteriol, 190, 5190-5198.  
18023805 M.Takeo, M.Nishimura, H.Takahashi, C.Kitamura, D.Kato, and S.Negoro (2007).
Purification and characterization of alkylcatechol 2,3-dioxygenase from butylphenol degradation pathway of Pseudomonas putida MT4.
  J Biosci Bioeng, 104, 309-314.  
17617714 M.Takeo, M.Nishimura, M.Shirai, H.Takahashi, and S.Negoro (2007).
Purification and characterization of catechol 2,3-dioxygenase from the aniline degradation pathway of Acinetobacter sp. YAA and its mutant enzyme, which resists substrate inhibition.
  Biosci Biotechnol Biochem, 71, 1668-1675.  
  16511281 K.Sugimoto, K.Matsufuzi, H.Ohnuma, M.Senda, M.Fukuda, and T.Senda (2006).
Crystallization and preliminary crystallographic analysis of the catechol 2,3-dioxygenase PheB from Bacillus stearothermophilus BR219.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 125-127.  
16734718 L.Siani, A.Viggiani, E.Notomista, A.Pezzella, and A.Di Donato (2006).
The role of residue Thr249 in modulating the catalytic efficiency and substrate specificity of catechol-2,3-dioxygenase from Pseudomonas stutzeri OX1.
  FEBS J, 273, 2963-2976.  
15730028 E.Tsirogianni, M.Aivaliotis, M.Karas, and G.Tsiotis (2005).
Detection and characterisation of catechol 2,3-dioxygenase in an indigenous soil pseudomonad by MALDI-TOF MS using a column separation.
  Biodegradation, 16, 181-186.  
16217642 J.P.Emerson, M.L.Wagner, M.F.Reynolds, L.Que, M.J.Sadowsky, and L.P.Wackett (2005).
The role of histidine 200 in MndD, the Mn(II)-dependent 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Arthrobacter globiformis CM-2, a site-directed mutagenesis study.
  J Biol Inorg Chem, 10, 751-760.  
15347689 A.Viggiani, L.Siani, E.Notomista, L.Birolo, P.Pucci, and A.Di Donato (2004).
The role of the conserved residues His-246, His-199, and Tyr-255 in the catalysis of catechol 2,3-dioxygenase from Pseudomonas stutzeri OX1.
  J Biol Chem, 279, 48630-48639.  
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
14756875 H.Junca, and D.H.Pieper (2004).
Functional gene diversity analysis in BTEX contaminated soils by means of PCR-SSCP DNA fingerprinting: comparative diversity assessment against bacterial isolates and PCR-DNA clone libraries.
  Environ Microbiol, 6, 95.  
15583384 K.Iwata, H.Noguchi, Y.Usami, J.W.Nam, Z.Fujimoto, H.Mizuno, H.Habe, H.Yamane, T.Omori, and H.Nojiri (2004).
Crystallization and preliminary crystallographic analysis of the 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase from the carbazole-degrader Pseudomonas resinovorans strain CA10.
  Acta Crystallogr D Biol Crystallogr, 60, 2340-2342.  
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
12728990 K.Iwata, H.Nojiri, K.Shimizu, T.Yoshida, H.Habe, and T.Omori (2003).
Expression, purification, and characterization of 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase from carbazole-degrader Pseudomonas resinovorans strain CA10.
  Biosci Biotechnol Biochem, 67, 300-307.  
12672826 T.Hatta, G.Mukerjee-Dhar, J.Damborsky, H.Kiyohara, and K.Kimbara (2003).
Characterization of a novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from a polychlorinated biphenyl- and naphthalene-degrading Bacillus sp. JF8.
  J Biol Chem, 278, 21483-21492.  
12039004 M.J.Ryle, and R.P.Hausinger (2002).
Non-heme iron oxygenases.
  Curr Opin Chem Biol, 6, 193-201.  
12121648 T.W.Martin, Z.Dauter, Y.Devedjiev, P.Sheffield, F.Jelen, M.He, D.H.Sherman, J.Otlewski, Z.S.Derewenda, and U.Derewenda (2002).
Molecular basis of mitomycin C resistance in streptomyces: structure and function of the MRD protein.
  Structure, 10, 933-942.
PDB codes: 1kll 1kmz
11470438 A.A.McCarthy, H.M.Baker, S.C.Shewry, M.L.Patchett, and E.N.Baker (2001).
Crystal structure of methylmalonyl-coenzyme A epimerase from P. shermanii: a novel enzymatic function on an ancient metal binding scaffold.
  Structure, 9, 637-646.
PDB codes: 1jc4 1jc5
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.  
11472911 I.J.Dinkla, E.M.Gabor, and D.B.Janssen (2001).
Effects of iron limitation on the degradation of toluene by Pseudomonas strains carrying the tol (pWWO) plasmid.
  Appl Environ Microbiol, 67, 3406-3412.  
11395407 J.A.Gerlt, and P.C.Babbitt (2001).
Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.
  Annu Rev Biochem, 70, 209-246.  
11578928 T.D.Bugg (2001).
Oxygenases: mechanisms and structural motifs for O(2) activation.
  Curr Opin Chem Biol, 5, 550-555.  
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
10986264 N.Hugo, C.Meyer, J.Armengaud, J.Gaillard, K.N.Timmis, and Y.Jouanneau (2000).
Characterization of three XylT-like [2Fe-2S] ferredoxins associated with catabolism of cresols or naphthalene: evidence for their involvement in catechol dioxygenase reactivation.
  J Bacteriol, 182, 5580-5585.  
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
10467142 L.Serre, A.Sailland, D.Sy, P.Boudec, A.Rolland, E.Pebay-Peyroula, and C.Cohen-Addad (1999).
Crystal structure of Pseudomonas fluorescens 4-hydroxyphenylpyruvate dioxygenase: an enzyme involved in the tyrosine degradation pathway.
  Structure, 7, 977-988.
PDB code: 1cjx
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 codes are shown on the right.