An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Pseudomonas putida mt-2

Kita, Akiko; Kita, Satomi; Fujisawa, Ikuhide; Inaka, Koji; Ishida, Tetsuo; Horiike, Kihachiro; Nozaki, Mitsuhiro; Miki, Kunio

doi:10.1016/s0969-2126(99)80006-9

Cited by 164 publications

(147 citation statements)

References 32 publications

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“…The ligand sphere of the Arabidopsis HPPD was not resolved at 3.0 Å ; however, there was clearly additional electron density at the iron atom that could not be satisfactorily explained by a single water molecule. The active site geometry of HPPD is very similar to that of the structurally related extradiol-cleaving catechol dioxygenase metapyrocatechase (Kita et al, 1999) and the biphenylcleaving extradiol dioxygenase DHBD (Han et al, 1995;Senda et al, 1996) although the latter enzymes have open active sites without a gating mechanism. All three enzymes share two His and a Glu residue as iron ligands.…”

Section: Active Site Architecturementioning

confidence: 90%

“…The comparison of all four modules shows a topology of babbba with larger variations at the second a-helix which is not surprising as it contains the moduleconnecting sequences. Despite the mechanistic relation to a-keto acid dependent dioxygenases, HPPD shares these structural features with one class of extradiol ring-cleaving dioxygenases that includes catechol-2,3-dioxygenase (Kita et al, 1999).…”

Section: Overall Fold Of Plant Hppdmentioning

confidence: 99%

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The Crystal Structures of Zea mays and Arabidopsis 4-Hydroxyphenylpyruvate Dioxygenase

et al. 2004

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The transformation of 4-hydroxyphenylpyruvate to homogentisate, catalyzed by 4-hydroxyphenylpyruvate dioxygenase (HPPD), plays an important role in degrading aromatic amino acids. As the reaction product homogentisate serves as aromatic precursor for prenylquinone synthesis in plants, the enzyme is an interesting target for herbicides. In this study we report the first x-ray structures of the plant HPPDs of Zea mays and Arabidopsis in their substrate-free form at 2.0 Å and 3.0 Å resolution, respectively. Previous biochemical characterizations have demonstrated that eukaryotic enzymes behave as homodimers in contrast to prokaryotic HPPDs, which are homotetramers. Plant and bacterial enzymes share the overall fold but use orthogonal surfaces for oligomerization. In addition, comparison of both structures provides direct evidence that the C-terminal helix gates substrate access to the active site around a nonheme ferrous iron center. In the Z. mays HPPD structure this helix packs into the active site, sequestering it completely from the solvent. In contrast, in the Arabidopsis structure this helix tilted by about 608 into the solvent and leaves the active site fully accessible. By elucidating the structure of plant HPPD enzymes we aim to provide a structural basis for the development of new herbicides.

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Section: Active Site Architecturementioning

confidence: 90%

Section: Overall Fold Of Plant Hppdmentioning

confidence: 99%

The Crystal Structures of Zea mays and Arabidopsis 4-Hydroxyphenylpyruvate Dioxygenase

et al. 2004

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“…1,2) The class II enzymes have two domains with similar folding patterns, as seem in the crystal structures of several class II extradiol dioxygenases. [3][4][5][6] In contrast, the amino acid sequences of class III dioxygenases are not similar to the sequences shared by the class II enzyme.…”

Section: Pseudomonas Resinovoransmentioning

confidence: 92%

“…strain KKS102, 4) BphC from Burkholderia sp. strain LB400, 5) and Mpc from P. putida strain mt-2, 6) have been found by X-ray crystallography. A model of CarB was constructed on the basis of the experimentally established structure of LigAB (PDB entry, 1BOU), 7) because both CarBaBb and LigAB are class III extradiol dioxygenases 1) that consist of two subunits.…”

Section: Molecular Mass Estimation and The Quaternary Structure Of Camentioning

confidence: 98%

Expression, Purification, and Characterization of 2′-Aminobiphenyl-2,3-diol 1,2-dioxygenase from Carbazole-degraderPseudomonas resinovoransStrain CA10

Iwata

Nojiri

Shimizu

et al. 2003

Bioscience, Biotechnology, and Biochemistry

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“…Type I enzymes can be further subdivided based on their preference for substrates that have one or two aromatic rings. The crystal structure of at least one member of each subclass has been solved: P. putida mt-2 2,3-CTD (40), which catalyzes the cleavage of monocyclic aromatics, and BPHC_LB400 (27) and BPHC_PS102 (68), which catalyze the cleavage of bicyclic aromatics. These structures demonstrate that these enzymes have a common fold, though different oligomeric structures.…”

mentioning

confidence: 99%

Crystallographic Comparison of Manganese- and Iron-Dependent Homoprotocatechuate 2,3-Dioxygenases

et al. 2004

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The X-ray crystal structures of homoprotocatechuate 2,3-dioxygenases isolated from Arthrobacter globiformis and Brevibacterium fuscum have been determined to high resolution. These enzymes exhibit 83% sequence identity, yet their activities depend on different transition metals, Mn 2؉ and Fe 2؉ , respectively. The structures allow the origins of metal ion selectivity and aspects of the molecular mechanism to be examined in detail. The homotetrameric enzymes belong to the type I family of extradiol dioxygenases (vicinal oxygen chelate superfamily); each monomer has four ␤␣␤␤␤ modules forming two structurally homologous N-terminal and C-terminal barrel-shaped domains. The active-site metal is located in the C-terminal barrel and is ligated by two equatorial ligands, H214 NE1 and E267 OE1 ; one axial ligand, H155 NE1 ; and two to three water molecules. The first and second coordination spheres of these enzymes are virtually identical (root mean square difference over all atoms, 0.19 Å), suggesting that the metal selectivity must be due to changes at a significant distance from the metal and/or changes that occur during folding. The substrate (2,3-dihydroxyphenylacetate [HPCA]) chelates the metal asymmetrically at sites trans to the two imidazole ligands and interacts with a unique, mobile C-terminal loop. The loop closes over the bound substrate, presumably to seal the active site as the oxygen activation process commences. An "open" coordination site trans to E267 is the likely binding site for O 2 . The geometry of the enzyme-substrate complexes suggests that if a transiently formed metal-superoxide complex attacks the substrate without dissociation from the metal, it must do so at the C-3 position. Second-sphere active-site residues that are positioned to interact with the HPCA and/or bound O 2 during catalysis are identified and discussed in the context of current mechanistic hypotheses.Bacterial ring-cleaving dioxygenases are critical enzymes in the catabolism of aromatic compounds that enter the environment from a myriad of sources (9,17,18,44). The substrates for most of these enzymes are ortho-or para-dihydroxylated aromatics and molecular oxygen. Both atoms of oxygen from O 2 are incorporated into the product as the ring is cleaved. The resulting aliphatic products are further metabolized to intermediates of core metabolic cycles through well-established pathways (18,55,74).Dioxygenases that act on ortho-dihydroxylated aromatic compounds are divided into two classes, termed intradiol and extradiol, which differ in their mode of ring cleavage and the oxidation state of the active-site metal (44, 63). Intradiol dioxygenases utilize Fe 3ϩ and cleave the bond between the carbons bearing the two hydroxyls; extradiol dioxygenases utilize Fe 2ϩ or, rarely, Mn 2ϩ and cleave one of the carbon-carbon bonds adjacent to the ortho-hydroxyl substituents. Although intradiol and extradiol dioxygenases oxidize an overlapping set of substrates, they are not structurally related and are proposed to have fundamentally differ...

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An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Pseudomonas putida mt-2

Cited by 164 publications

References 32 publications

The Crystal Structures of Zea mays and Arabidopsis 4-Hydroxyphenylpyruvate Dioxygenase

The Crystal Structures of Zea mays and Arabidopsis 4-Hydroxyphenylpyruvate Dioxygenase

Expression, Purification, and Characterization of 2′-Aminobiphenyl-2,3-diol 1,2-dioxygenase from Carbazole-degraderPseudomonas resinovoransStrain CA10

Crystallographic Comparison of Manganese- and Iron-Dependent Homoprotocatechuate 2,3-Dioxygenases

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