spacer
spacer
Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Dioxygenase PDB id
1b4u
Jmol
Contents
Protein chains
132 a.a. *
298 a.a. *
Ligands
DHB ×2
Metals
_FE ×2
Waters ×189
* Residue conservation analysis
PDB id:
1b4u
Name: Dioxygenase
Title: Protocatechuate 4,5-dioxygenase (ligab) in complex with protocatechuate (pca)
Structure: Protocatechuate 4,5-dioxygenase. Chain: a, c. Fragment: chain a, c, alpha chain, chain b, d, beta chain. Synonym: liga, ligb. Engineered: yes. Protocatechuate 4,5-dioxygenase. Chain: b, d. Fragment: chain a, c, alpha chain, chain b, d, beta chain. Synonym: liga, ligb.
Source: Sphingomonas paucimobilis. Organism_taxid: 13689. Strain: syk-6. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.20Å     R-factor:   0.161     R-free:   0.220
Authors: K.Sugimoto,T.Senda,Y.Mitsui
Key ref:
K.Sugimoto et al. (1999). Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions. Structure, 7, 953-965. PubMed id: 10467151 DOI: 10.1016/S0969-2126(99)80122-1
Date:
29-Dec-98     Release date:   27-Aug-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P22635  (PCYA_PSEPA) -  Protocatechuate 4,5-dioxygenase alpha chain
Seq:
Struc: 		139 a.a.
132 a.a.
Protein chains
Pfam   ArchSchema ?
P22636  (PCYB_PSEPA) -  Protocatechuate 4,5-dioxygenase beta chain
Seq:
Struc: 		302 a.a.
298 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.1.13.11.8  - Protocatechuate 4,5-dioxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protocatechuate + O2 = 4-carboxy-2-hydroxymuconate semialdehyde
Protocatechuate
Bound ligand (Het Group name = DHB)
corresponds exactly 		+ O(2)
 = 4-carboxy-2-hydroxymuconate semialdehyde
      Cofactor: Iron
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation reduction   3 terms 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(99)80122-1 Structure 7:953-965 (1999)
PubMed id: 10467151  
 
 
Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions.
K.Sugimoto, T.Senda, H.Aoshima, E.Masai, M.Fukuda, Y.Mitsui.
 
  ABSTRACT  
 
BACKGROUND: Sphingomonas paucimobilis SYK-6 utilizes an extradiol-type catecholic dioxygenase, the LigAB enzyme (a protocatechuate 4,5-dioxygenase), to oxidize protocatechuate (or 3,4-dihydroxybenzoic acid, PCA). The enzyme belongs to the family of class III extradiol-type catecholic dioxygenases catalyzing the ring-opening reaction of protocatechuate and related compounds. The primary structure of LigAB suggests that the enzyme has no evolutionary relationship with the family of class II extradiol-type catecholic dioxygenases. Both the class II and class III enzymes utilize a non-heme ferrous center for adding dioxygen to the substrate. By elucidating the structure of LigAB, we aimed to provide a structural basis for discussing the function of class III enzymes. RESULTS: The crystal structure of substrate-free LigAB was solved at 2.2 A resolution. The molecule is an alpha2beta2 tetramer. The active site contains a non-heme iron coordinated by His12, His61, Glu242, and a water molecule located in a deep cleft of the beta subunit, which is covered by the alpha subunit. Because of the apparent oxidation of the Fe ion into the nonphysiological Fe(III) state, we could also solve the structure of LigAB complexed with a substrate, PCA. The iron coordination sphere in this complex is a distorted tetragonal bipyramid with one ligand missing, which is presumed to be the O2-binding site. CONCLUSIONS: The structure of LigAB is completely different from those of the class II extradiol-type dioxygenases exemplified by the BphC enzyme, a 2,3-dihydroxybiphenyl 1,2-dioxygenase from a Pseudomonas species. Thus, as already implicated by the primary structures, no evolutionary relationship exists between the class II and III enzymes. However, the two classes of enzymes share many geometrical characteristics with respect to the nature of the iron coordination sphere and the position of a putative catalytic base, strongly suggesting a common catalytic mechanism.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Stereoview Ca trace of (a) the a subunit and (b) the b subunit. The Fe ion in the b subunit is shown as a shaded sphere. The arrow indicates the site of insertion of a long loop in some of the class III dioxygenases (see text). (These figures were prepared using the program MOLSCRIPT [36].)
 
  The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 953-965) copyright 1999.  
  Figure was selected by the author.  

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.  
20860734 R.Vilchez-Vargas, H.Junca, and D.H.Pieper (2010).
Metabolic networks, microbial ecology and 'omics' technologies: towards understanding in situ biodegradation processes.
  Environ Microbiol, 12, 3089-3104.  
19717587 D.Kasai, T.Fujinami, T.Abe, K.Mase, Y.Katayama, M.Fukuda, and E.Masai (2009).
Uncovering the protocatechuate 2,3-cleavage pathway genes.
  J Bacteriol, 191, 6758-6768.  
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.  
19575758 M.V.Brennerova, J.Josefiova, V.Brenner, D.H.Pieper, and H.Junca (2009).
Metagenomics reveals diversity and abundance of meta-cleavage pathways in microbial communities from soil highly contaminated with jet fuel under air-sparging bioremediation.
  Environ Microbiol, 11, 2216-2227.  
18045866 C.Qiu, S.Lienhard, N.E.Hynes, A.Badache, and D.J.Leahy (2008).
Memo Is Homologous to Nonheme Iron Dioxygenases and Binds an ErbB2-derived Phosphopeptide in Its Vestigial Active Site.
  J Biol Chem, 283, 2734-2740.
PDB codes: 3bcz 3bd0
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.  
18502867 M.J.Moonen, S.A.Synowsky, W.A.van den Berg, A.H.Westphal, A.J.Heck, R.H.van den Heuvel, M.W.Fraaije, and W.J.van Berkel (2008).
Hydroquinone dioxygenase from pseudomonas fluorescens ACB: a novel member of the family of nonheme-iron(II)-dependent dioxygenases.
  J Bacteriol, 190, 5199-5209.  
18249197 T.D.Bugg, and S.Ramaswamy (2008).
Non-heme iron-dependent dioxygenases: unravelling catalytic mechanisms for complex enzymatic oxidations.
  Curr Opin Chem Biol, 12, 134-140.  
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.  
17390132 J.D.Awaya, C.Walton, and D.Borthakur (2007).
The pydA-pydB fusion gene produces an active dioxygenase-hydrolase that degrades 3-hydroxy-4-pyridone, an intermediate of mimosine metabolism.
  Appl Microbiol Biotechnol, 75, 583-588.  
16583229 D.Zhen, H.Liu, S.J.Wang, J.J.Zhang, F.Zhao, and N.Y.Zhou (2006).
Plasmid-mediated degradation of 4-chloronitrobenzene by newly isolated Pseudomonas putida strain ZWL73.
  Appl Microbiol Biotechnol, 72, 797-803.  
17051653 J.Schlosrich, K.L.Eley, P.J.Crowley, and T.D.Bugg (2006).
Directed evolution of a non-heme-iron-dependent extradiol catechol dioxygenase: identification of mutants with intradiol oxidative cleavage activity.
  Chembiochem, 7, 1899-1908.  
16030198 D.Kasai, E.Masai, K.Miyauchi, Y.Katayama, and M.Fukuda (2005).
Characterization of the gallate dioxygenase gene: three distinct ring cleavage dioxygenases are involved in syringate degradation by Sphingomonas paucimobilis SYK-6.
  J Bacteriol, 187, 5067-5074.  
15580337 J.F.Wu, C.W.Sun, C.Y.Jiang, Z.P.Liu, and S.J.Liu (2005).
A novel 2-aminophenol 1,6-dioxygenase involved in the degradation of p-chloronitrobenzene by Comamonas strain CNB-1: purification, properties, genetic cloning and expression in Escherichia coli.
  Arch Microbiol, 183, 1-8.  
16030014 J.Nogales, A.Canales, J.Jiménez-Barbero, J.L.García, and E.Díaz (2005).
Molecular characterization of the gallate dioxygenase from Pseudomonas putida KT2440. The prototype of a new subgroup of extradiol dioxygenases.
  J Biol Chem, 280, 35382-35390.  
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.  
15739104 K.D.Koehntop, J.P.Emerson, and L.Que (2005).
The 2-His-1-carboxylate facial triad: a versatile platform for dioxygen activation by mononuclear non-heme iron(II) enzymes.
  J Biol Inorg Chem, 10, 87-93.  
15672171 S.Mendel, A.Arndt, and T.D.Bugg (2005).
Lactone synthesis activity in a site-directed mutant of an extradiol catechol dioxygenase enzyme.
  Chem Commun (Camb), 0, 666-668.  
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
15262932 D.Kasai, E.Masai, K.Miyauchi, Y.Katayama, and M.Fukuda (2004).
Characterization of the 3-O-methylgallate dioxygenase gene and evidence of multiple 3-O-methylgallate catabolic pathways in Sphingomonas paucimobilis SYK-6.
  J Bacteriol, 186, 4951-4959.  
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.  
15277747 K.Maruyama, T.Shibayama, A.Ichikawa, Y.Sakou, S.Yamada, and H.Sugisaki (2004).
Cloning and characterization of the genes encoding enzymes for the protocatechuate meta-degradation pathway of Pseudomonas ochraceae NGJ1.
  Biosci Biotechnol Biochem, 68, 1434-1441.  
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.  
  12039004 M.J.Ryle, and R.P.Hausinger (2002).
Non-heme iron oxygenases.
  Curr Opin Chem Biol, 6, 193-201.  
12224629 T.Iida, Y.Mukouzaka, K.Nakamura, I.Yamaguchi, and T.Kudo (2002).
Isolation and characterization of dibenzofuran-degrading actinomycetes: analysis of multiple extradiol dioxygenase genes in dibenzofuran-degrading Rhodococcus species.
  Biosci Biotechnol Biochem, 66, 1462-1472.  
11729263 E.Díaz, A.Ferrández, M.A.Prieto, and J.L.García (2001).
Biodegradation of aromatic compounds by Escherichia coli.
  Microbiol Mol Biol Rev, 65, 523.  
  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
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.  
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.