Three-dimensional Structures of Free Form and Two Substrate Complexes of an Extradiol Ring-cleavage Type Dioxygenase, the BphC Enzyme fromPseudomonassp. Strain KKS102

Senda, Toshiya; Sugiyama, Kazuyuki; Narita, Hiroki; Yamamoto, Takeshi; Kimbara, Kazuhide; Fukuda, Masao; Sato, Mitsuo; Yano, Keiji; Mitsui, Yukio

doi:10.1006/jmbi.1996.0060

Cited by 209 publications

(179 citation statements)

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“…This is the first step in a pathway leading to complete oxidation of CH 4 to CO 2 that satisfies the carbon and energy needs of the bacterium. Although all methanotrophs can elaborate a membrane bound, copper-containing form of MMO, many type II and X methanotrophs produce exclusively a soluble, iron-containing form (sMMO) in a low copper environment.…”

Section: Methane Monooxygenase Overview Of the Structure And Mechanismmentioning

confidence: 99%

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Finding Intermediates in the O₂ Activation Pathways of Non-Heme Iron Oxygenases

et al. 2007

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Intermediates in the reaction cycle of an oxygenase are usually very informative of the chemical mechanism of O 2 activation and insertion. However, detection of these intermediates is often complicated by their short lifetime and the regulatory mechanism of the enzyme designed to ensure specificity. Here, the methods used to detect the intermediates in an extradiol dioxygenase, a Rieske cis-dihydrodiol dioxygenase, and soluble methane monooxygenase are discussed. The methods include the use of alternative, chromophoric substrates, mutagenesis of active site catalytic residues, forced changes in substrate binding order, control of reaction rates using regulatory proteins, and initialization of catalysis in crystallo.

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Section: Methane Monooxygenase Overview Of the Structure And Mechanismmentioning

confidence: 99%

“…2,4,[6][7][8][9] This directly displaces two solvents from the "catalytic" face of the facial triad. The third solvent bond to the iron (if present) is weakened or broken by the donation of charge from the anionic catecholic ligand.…”

Section: Introductionmentioning

confidence: 99%

Finding Intermediates in the O₂ Activation Pathways of Non-Heme Iron Oxygenases

et al. 2007

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“…In the latter case, site-directed mutagenesis was used to demonstrate that these three amino acids are essential for dioxygenase activity [ 1 I]. Crystallographic studies on the enzyme-substrate complex show that the substrate coordinates in a bidentate manner [4], as deduced from extended X-ray ab- sorption fine-structure studies of catechol 2,3-dioxygenase [12].…”

Section: The 2-his-1-carboxylate Facial Triadmentioning

confidence: 99%

The 2‐His‐1‐Carboxylate Facial Triad — An Emerging Structural Motif in Mononuclear Non‐Heme Iron(II) Enzymes

Hegg

Que

1997

European Journal of Biochemistry

522

467

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A 2-His-I-carboxylate facial triad is a common feature of the active sites in a number of mononuclear non-heme iron(I1) enzymes. This structural motif was established crystallographically for five different classes of enzymes and inferred from sequence similarity for two other classes. The 2-His-1-carboxylate facial triad anchors the iron in the active site and at the same time maintains three additional cis-oriented sites. These sites can be used to bind other endogenous ligands or exogenous ligands such as substrate and/or 02, giving the metal center great flexibility to use different mechanistic strategies to perform a variety of chemical transformations.Keywords: 2-His-I -carboxylate facial triad; non-heme; oxygenase; iron ; mononuclear.Mononuclear non-heme iron(I1) enzymes catalyze a diverse range of important reactions in the metabolism of amino acids, nucleic acids, and fatty acids, the biodegradation of aromatic compounds, and the biosynthesis of antibiotics such as penicillin and cephalosporin (Fig. 1) [ I , 21. This emerging class of enzymes now rivals heme enzymes in the diversity of oxidative transformations catalyzed. While many of the mechanistic strategies employed by these two classes of enzymes are similar, there are some significant differences. Heme enzymes feature an iron porphyrin cofactor that is ligated to an amino acid residue on the polypeptide chain; such a ligand environment leaves only one coordination site available for the binding of exogenous ligands, typically 0, for dioxygen-activating enzymes. As a consequence, NADH is the usual source of the two electrons needed for the reaction and a reductase is required to mediate electron transfer into the heme active site. In contrast, mononuclear nonheme iron enzymes employ a variety of electron sources, often metal-bound substrates or cofactors, to reduce 0, to the peroxide oxidation state. This mechanistic feature requires a more flexible metal-coordination environment to allow for the binding of a number of exogenous ligands. Understanding how the ligand environment around the metal center in mononuclear non-heme iron enzymes affects their chemistry and allows them to perform reactions typically associated with their heme counterparts is an area of intense current interest. Emerging from recent crystallographic studies on mononuclear non-heme enzymes is a com-

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“…In addition, the determination of the crystal structures of 2,3-dihydroxybiphenyl dioxygenase from Pseudomonas cepacia LB400 (BphC_LB400) (16) and Pseudomonas sp. strain KKS102 (BphC_PS102) (38) revealed that these enzymes include homologous N-and C-terminal domains, each of which is constructed from two ␤␣␤␤␤ motifs. Although this observation enabled us to propose that the smaller dioxygenases represent single-domain homologs of the better-characterized, larger enzymes, the evolutionary relationship between these families was not established (16).…”

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Evolutionary relationships among extradiol dioxygenases

1996

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A structure-validated alignment of 35 extradiol dioxygenase sequences including two-domain and onedomain enzymes was derived. Strictly conserved residues include the metal ion ligands and several catalytically essential active site residues, as well as a number of structurally important residues that are remote from the active site. Phylogenetic analyses based on this alignment indicate that the ancestral extradiol dioxygenase was a one-domain enzyme and that the two-domain enzymes arose from a single genetic duplication event. Subsequent divergence among the two-domain dioxygenases has resulted in several families, two of which are based on substrate preference. In several cases, the two domains of a given enzyme express different phylogenies, suggesting the possibility that such enzymes arose from the recombination of genes encoding different dioxygenases. A phylogeny-based classification system for extradiol dioxygenases is proposed.Dioxygenases catalyse the incorporation of both atoms of dioxygen into their substrates. These enzymes are widely distributed in nature and are involved in both anabolic and catabolic processes (21). One important catabolic process is the aerobic degradation of aromatic compounds by bacteria wherein dioxygenases catalyse two critical reactions: ring dihydroxylation and ring cleavage. A typical substrate of the latter reaction is a catecholic metabolite possessing hydroxyl substituents on two adjacent carbon atoms. Cleavage is generally catalyzed by metalloenzymes of one of two functional classes. Intradiol dioxygenases cleave ortho to the hydroxyl substituents and typically depend on nonheme Fe(III). In contrast, extradiol dioxygenases cleave meta to the hydroxyl substituents and typically depend on nonheme Fe(II). Although these distinctions may appear to be minor, they are in fact a manifestation of enzymes that have completely different structures and exclusively utilize different mechanisms (18).While it is clear that the intra-and extradiol enzymes have arisen from different ancestors, the evolutionary relationships within each group are less well defined. Several years ago, Harayama and Rekik (19) proposed that the extradiol dioxygenases could be divided into two families: those showing a preference for bicyclic substrates and those showing a preference for monocyclic substrates. Since that time, the sequences and characteristics of a large number of extradiol dioxygenases have been established, and the first three-dimensional structures have been determined; it is now clear that further study of the evolutionary relationships is warranted. For example, a new family of smaller, Fe-dependent, extradiol dioxygenases (3) and a Mn-containing dioxygenase similar to the Fe-containing enzymes (8) have been recently described. In addition, the determination of the crystal structures of 2,3-dihydroxybiphenyl dioxygenase from Pseudomonas cepacia LB400 (BphC_LB400) (16) and Pseudomonas sp. strain KKS102 (BphC_PS102) (38) revealed that these enzymes include homologous N-and C-terminal ...

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Three-dimensional Structures of Free Form and Two Substrate Complexes of an Extradiol Ring-cleavage Type Dioxygenase, the BphC Enzyme fromPseudomonassp. Strain KKS102

Cited by 209 publications

References 0 publications

Finding Intermediates in the O₂ Activation Pathways of Non-Heme Iron Oxygenases

Finding Intermediates in the O₂ Activation Pathways of Non-Heme Iron Oxygenases

The 2‐His‐1‐Carboxylate Facial Triad — An Emerging Structural Motif in Mononuclear Non‐Heme Iron(II) Enzymes

Evolutionary relationships among extradiol dioxygenases

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Three-dimensional Structures of Free Form and Two Substrate Complexes of an Extradiol Ring-cleavage Type Dioxygenase, the BphC Enzyme fromPseudomonassp. Strain KKS102

Cited by 209 publications

References 0 publications

Finding Intermediates in the O2 Activation Pathways of Non-Heme Iron Oxygenases

Finding Intermediates in the O2 Activation Pathways of Non-Heme Iron Oxygenases

The 2‐His‐1‐Carboxylate Facial Triad — An Emerging Structural Motif in Mononuclear Non‐Heme Iron(II) Enzymes

Evolutionary relationships among extradiol dioxygenases

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Finding Intermediates in the O₂ Activation Pathways of Non-Heme Iron Oxygenases

Finding Intermediates in the O₂ Activation Pathways of Non-Heme Iron Oxygenases