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Oxidoreductase PDB id
1t0r
Jmol
Contents
Protein chains
491 a.a. *
323 a.a. *
84 a.a. *
Ligands
_OH
AZI
Metals
_FE ×2
Waters ×345
* Residue conservation analysis
PDB id:
1t0r
Name: Oxidoreductase
Title: Crystal structure of the toluene/o-xylene monooxygenase hydroxuylase from pseudomonas stutzeri-azide bound
Structure: Toluene, o-xylene monooxygenase oxygenase subunit. Chain: a. Engineered: yes. Other_details: alpha subunit. Toluene, o-xylene monooxygenase oxygenase subunit. Chain: b. Engineered: yes.
Source: Pseudomonas stutzeri. Organism_taxid: 316. Gene: toua. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: toue. Gene: toub.
Biol. unit: Trimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.218     R-free:   0.267
Authors: M.H.Sazinsky,J.Bard,A.Di Donato,S.J.Lippard
Key ref:
M.H.Sazinsky et al. (2004). Crystal structure of the toluene/o-xylene monooxygenase hydroxylase from Pseudomonas stutzeri OX1. Insight into the substrate specificity, substrate channeling, and active site tuning of multicomponent monooxygenases. J Biol Chem, 279, 30600-30610. PubMed id: 15096510 DOI: 10.1074/jbc.M400710200
Date:
12-Apr-04     Release date:   27-Jul-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O87798  (O87798_PSEST) -  Toluene, o-xylene monooxygenase oxygenase subunit
Seq:
Struc: 		498 a.a.
491 a.a.
Protein chain
Pfam   ArchSchema ?
O87802  (O87802_PSEST) -  Toluene, o-xylene monooxygenase oxygenase subunit
Seq:
Struc: 		330 a.a.
323 a.a.
Protein chain
Pfam   ArchSchema ?
O87799  (O87799_PSEST) -  TouB protein
Seq:
Struc: 		86 a.a.
84 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation reduction   2 terms 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
DOI no: 10.1074/jbc.M400710200 J Biol Chem 279:30600-30610 (2004)
PubMed id: 15096510  
 
 
Crystal structure of the toluene/o-xylene monooxygenase hydroxylase from Pseudomonas stutzeri OX1. Insight into the substrate specificity, substrate channeling, and active site tuning of multicomponent monooxygenases.
M.H.Sazinsky, J.Bard, A.Di Donato, S.J.Lippard.
 
  ABSTRACT  
 
The four-component toluene/o-xylene monooxygenase (ToMO) from Pseudomonas stutzeri OX1 is capable of oxidizing arenes, alkenes, and haloalkanes at a carboxylate-bridged diiron center similar to that of soluble methane monooxygenase (sMMO). The remarkable variety of substrates accommodated by ToMO invites applications ranging from bioremediation to the regio- and enantiospecific oxidation of hydrocarbons on an industrial scale. We report here the crystal structures of the ToMO hydroxylase (ToMOH), azido ToMOH, and ToMOH containing the product analogue 4-bromophenol to 2.3 A or greater resolution. The catalytic diiron(III) core resembles that of the sMMO hydroxylase, but aspects of the alpha2beta2gamma2 tertiary structure are notably different. Of particular interest is a 6-10 A-wide channel of approximately 35 A in length extending from the active site to the protein surface. The presence of three bromophenol molecules in this space confirms this route as a pathway for substrate entrance and product egress. An analysis of the ToMOH active site cavity offers insights into the different substrate specificities of multicomponent monooxygenases and explains the behavior of mutant forms of homologous enzymes described in the literature.
 
  Selected figure(s)  
 
Figure 3.
FIG. 3. Hydrogen bonding at or near the ToMOH and MMOH diiron centers. Hydrogen bond interactions to the coordinated glutamate ligands of ToMOH (a) and MMOH (b). Atoms are colored as in Fig. 2a. c and d, the conserved hydrogen bonding network behind the histidine ligands in ToMOH (c) and MMOH (d). Amino acid residues are depicted in stick form and are colored by atom type. Ribbons are colored in green, and hydrogen bonds are presented as yellow dashes. 		Figure 5.
FIG. 5. The ToMOH substrate channel. a, location of the ToMOH channel openings on the surface of the protein in yellow. The subunits are colored as described in Fig. 1a. b, surface representation of the ToMOH -subunit channel colored by atom type in stereo. The diiron center is represented by orange spheres. The N and C termini and helices A-H are labeled.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 30600-30610) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21221457 D.R.Boyd, N.D.Sharma, P.J.Stevenson, M.Blain, C.McRoberts, J.T.Hamilton, J.M.Argudo, H.Mundi, L.A.Kulakov, and C.C.Allen (2011).
Dioxygenase-catalysed cis-dihydroxylation of meta-substituted phenols to yield cyclohexenone cis-diol and derived enantiopure cis-triol metabolites.
  Org Biomol Chem, 9, 1479-1490.  
20485834 S.Friedle, E.Reisner, and S.J.Lippard (2010).
Current challenges of modeling diiron enzyme active sites for dioxygen activation by biomimetic synthetic complexes.
  Chem Soc Rev, 39, 2768-2779.  
19074607 E.Notomista, V.Cafaro, G.Bozza, and A.Di Donato (2009).
Molecular determinants of the regioselectivity of toluene/o-xylene monooxygenase from Pseudomonas sp. strain OX1.
  Appl Environ Microbiol, 75, 823-836.  
19610611 J.R.Frisch, V.V.Vu, M.Martinho, E.Münck, and L.Que (2009).
Characterization of two distinct adducts in the reaction of a nonheme diiron(II) complex with O2.
  Inorg Chem, 48, 8325-8336.  
19757795 S.Friedle, J.J.Kodanko, A.J.Morys, T.Hayashi, P.Moënne-Loccoz, and S.J.Lippard (2009).
Modeling the syn disposition of nitrogen donors in non-heme diiron enzymes. Synthesis, characterization, and hydrogen peroxide reactivity of diiron(III) complexes with the syn N-donor ligand H2BPG2DEV.
  J Am Chem Soc, 131, 14508-14520.  
  20376288 S.Friedle, and S.J.Lippard (2009).
Synthesis, Characterization, and Oxygenation Studies of Carboxylate-Bridged Diiron(II) Complexes with Aromatic Substrates Tethered to Pyridine Ligands and the Formation of a Unique Trinuclear Complex.
  Eur J Inorg Chem, 2009, 5506-5515.  
19354250 W.J.Song, R.K.Behan, S.G.Naik, B.H.Huynh, and S.J.Lippard (2009).
Characterization of a peroxodiiron(III) intermediate in the T201S variant of toluene/o-xylene monooxygenase hydroxylase from Pseudomonas sp. OX1.
  J Am Chem Soc, 131, 6074-6075.  
18192418 R.Feingersch, J.Shainsky, T.K.Wood, and A.Fishman (2008).
Protein engineering of toluene monooxygenases for synthesis of chiral sulfoxides.
  Appl Environ Microbiol, 74, 1555-1566.  
19915653 S.Friedle, J.J.Kodanko, K.L.Fornace, and S.J.Lippard (2008).
9-Triptycenecarboxylate-Bridged Diiron(II) Complexes: Capture of the Paddlewheel Geometric Isomer.
  J Mol Struct, 890, 317-327.  
17605815 A.M.Burroughs, S.Balaji, L.M.Iyer, and L.Aravind (2007).
Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold.
  Biol Direct, 2, 18.  
17704278 E.Borodina, T.Nichol, M.G.Dumont, T.J.Smith, and J.C.Murrell (2007).
Mutagenesis of the "leucine gate" to explore the basis of catalytic versatility in soluble methane monooxygenase.
  Appl Environ Microbiol, 73, 6460-6467.  
18044971 L.J.Murray, R.García-Serres, M.S.McCormick, R.Davydov, S.G.Naik, S.H.Kim, B.M.Hoffman, B.H.Huynh, and S.J.Lippard (2007).
Dioxygen activation at non-heme diiron centers: oxidation of a proximal residue in the I100W variant of toluene/o-xylene monooxygenase hydroxylase.
  Biochemistry, 46, 14795-14809.
PDB code: 2rdb
17967027 L.J.Murray, S.G.Naik, D.O.Ortillo, R.García-Serres, J.K.Lee, B.H.Huynh, and S.J.Lippard (2007).
Characterization of the arene-oxidizing intermediate in ToMOH as a diiron(III) species.
  J Am Chem Soc, 129, 14500-14510.  
17288367 M.Newcomb, D.S.Lansakara-P, H.Y.Kim, R.E.Chandrasena, S.J.Lippard, L.G.Beauvais, L.J.Murray, V.Izzo, P.F.Hollenberg, and M.J.Coon (2007).
Products from enzyme-catalyzed oxidations of norcarenes.
  J Org Chem, 72, 1128-1133.  
16819737 H.Wade, S.E.Stayrook, and W.F.Degrado (2006).
The structure of a designed diiron(III) protein: implications for cofactor stabilization and catalysis.
  Angew Chem Int Ed Engl, 45, 4951-4954.  
16760312 J.Lalucat, A.Bennasar, R.Bosch, E.García-Valdés, and N.J.Palleroni (2006).
Biology of Pseudomonas stutzeri.
  Microbiol Mol Biol Rev, 70, 510-547.  
16788204 K.H.Halsey, L.A.Sayavedra-Soto, P.J.Bottomley, and D.J.Arp (2006).
Site-directed amino acid substitutions in the hydroxylase alpha subunit of butane monooxygenase from Pseudomonas butanovora: Implications for substrates knocking at the gate.
  J Bacteriol, 188, 4962-4969.  
16756297 L.J.Murray, R.García-Serres, S.Naik, B.H.Huynh, and S.J.Lippard (2006).
Dioxygen activation at non-heme diiron centers: characterization of intermediates in a mutant form of toluene/o-xylene monooxygenase hydroxylase.
  J Am Chem Soc, 128, 7458-7459.  
16859499 L.M.Iyer, A.M.Burroughs, and L.Aravind (2006).
The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains.
  Genome Biol, 7, R60.  
17176061 M.H.Sazinsky, P.W.Dunten, M.S.McCormick, A.DiDonato, and S.J.Lippard (2006).
X-ray structure of a hydroxylase-regulatory protein complex from a hydrocarbon-oxidizing multicomponent monooxygenase, Pseudomonas sp. OX1 phenol hydroxylase.
  Biochemistry, 45, 15392-15404.
PDB codes: 2inn 2inp
17117860 M.S.McCormick, M.H.Sazinsky, K.L.Condon, and S.J.Lippard (2006).
X-ray crystal structures of manganese(II)-reconstituted and native toluene/o-xylene monooxygenase hydroxylase reveal rotamer shifts in conserved residues and an enhanced view of the protein interior.
  J Am Chem Soc, 128, 15108-15110.
PDB codes: 2inc 2ind
17012379 P.M.Brown, T.T.Caradoc-Davies, J.M.Dickson, G.J.Cooper, K.M.Loomes, and E.N.Baker (2006).
Crystal structure of a substrate complex of myo-inositol oxygenase, a di-iron oxygenase with a key role in inositol metabolism.
  Proc Natl Acad Sci U S A, 103, 15032-15037.
PDB code: 2huo
15929999 D.H.Dyer, K.S.Lyle, I.Rayment, and B.G.Fox (2005).
X-ray structure of putative acyl-ACP desaturase DesA2 from Mycobacterium tuberculosis H37Rv.
  Protein Sci, 14, 1508-1517.
PDB code: 1za0
15687216 G.Vardar, and T.K.Wood (2005).
Alpha-subunit positions methionine 180 and glutamate 214 of Pseudomonas stutzeri OX1 toluene-o-xylene monooxygenase influence catalysis.
  J Bacteriol, 187, 1511-1514.  
15696279 G.Vardar, and T.K.Wood (2005).
Protein engineering of toluene-o-xylene monooxygenase from Pseudomonas stutzeri OX1 for enhanced chlorinated ethene degradation and o-xylene oxidation.
  Appl Microbiol Biotechnol, 68, 510-517.  
16116657 G.Vardar, Y.Tao, J.Lee, and T.K.Wood (2005).
Alanine 101 and alanine 110 of the alpha subunit of Pseudomonas stutzeri OX1 toluene-o-xylene monooxygenase influence the regiospecific oxidation of aromatics.
  Biotechnol Bioeng, 92, 652-658.  
15700297 J.R.Calhoun, F.Nastri, O.Maglio, V.Pavone, A.Lombardi, and W.F.DeGrado (2005).
Artificial diiron proteins: from structure to function.
  Biopolymers, 80, 264-278.  
16033515 J.Y.Kim, J.K.Kim, S.O.Lee, C.K.Kim, and K.Lee (2005).
Multicomponent phenol hydroxylase-catalysed formation of hydroxyindoles and dyestuffs from indole and its derivatives.
  Lett Appl Microbiol, 41, 163-168.  
16244735 S.Taktak, M.Flook, B.M.Foxman, L.Que, and E.V.Rybak-Akimova (2005).
Ortho-hydroxylation of benzoic acids with hydrogen peroxide at a non-heme iron center.
  Chem Commun (Camb), 0, 5301-5303.  
16085871 V.Cafaro, E.Notomista, P.Capasso, and A.Di Donato (2005).
Mutation of glutamic acid 103 of toluene o-xylene monooxygenase as a means to control the catabolic efficiency of a recombinant upper pathway for degradation of methylated aromatic compounds.
  Appl Environ Microbiol, 71, 4744-4750.  
15943801 W.L.Fosdike, T.J.Smith, and H.Dalton (2005).
Adventitious reactions of alkene monooxygenase reveal common reaction pathways and component interactions among bacterial hydrocarbon oxygenases.
  FEBS J, 272, 2661-2669.  
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.