Crystal Structures of the Reaction Intermediate and its Homologue of an Extradiol-cleaving Catecholic Dioxygenase

Sato, Nobuyuki; Uragami, Y.; Nishizaki, Terukazu; Takahashi, Yoshito; Sazaki, Gen; Sugimoto, Keisuke; Nonaka, Takamasa; Masai, Eiji; Fukuda, Masao; Senda, Toshiya

doi:10.1016/s0022-2836(02)00673-3

Cited by 105 publications

(135 citation statements)

References 31 publications

Supporting

Mentioning

123

Contrasting

Order By: Relevance

“…To identify and compare signature amino-acid sequences of amplified extradiol dioxygenases, a peptide sequence alignment was compared to the three-dimensional structure of BphC enzyme from Pseudomonas KKS102 (Sato et al, 2002) belonging to the group I.3.A (Eltis and Bolin, 1996). A simultaneous comparison of the alignment with the three-dimensional structure was made using the Cn3D v. 4.1 program (http://130.14.29.110/ Structure/CN3D/cn3d.shtml).…”

Section: Discussionmentioning

confidence: 99%

“…The peptide alignment (78 environmental sequences) was mapped to the three-dimensional structure of the BphC enzyme from Pseudomonas sp. KKS102 (Sato et al, 2002) to detect where the conserved amino acids are situated in the structure (data not shown). In the alignment of peptides, we identified two conserved regions, one b-sheet structure located between two domains that can be structurally important or involved in interactions between the domains and another region that is a loop on the surface of the enzyme connecting the N-and Cterminal domain.…”

Section: In Silico Hhai Fragmentsmentioning

confidence: 99%

“…The deduced amino-acid fragment peptide (154 amino acids) corresponds to the almost complete Nterminal part of the intact enzyme, and included the His145, crucial for iron binding in the catalytic centre (Sato et al, 2002). The BP-F sequence is 5 0 -TCTAYCTVCGNATGGAYHDBTGGCA-3 0 and BP-R 5 0 -TGVTSNCGNBCRTTGCARTGCATGAA-3 0 .…”

Section: Dna Isolation and Pcr Amplificationmentioning

confidence: 99%

See 2 more Smart Citations

High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil

Sipilä

Keskinen²,

Akerman³

et al. 2008

The ISME Journal

View full text Add to dashboard Cite

Genes encoding key enzymes of catabolic pathways can be targeted by DNA fingerprinting to explore genetic degradation potential in pristine and polluted soils. We performed a greenhouse microcosm experiment to elucidate structural and functional bacterial diversity in polyaromatic hydrocarbon (PAH)-polluted soil and to test the suitability of birch (Betula pendula) for remediation. Degradation of PAHs was analysed by high-performance liquid chromatography, DNA isolated from soil amplified and fingerprinted by restriction fragment length polymorphism (RFLP) and terminal restriction fragment length polymorphism (T-RFLP). Bacterial 16S rRNA T-RFLP fingerprinting revealed a high structural bacterial diversity in soil where PAH amendment altered the general community structure as well as the rhizosphere community. Birch augmented extradiol dioxygenase diversity in rhizosphere showing a rhizosphere effect, and further pyrene was more efficiently degraded in planted pots. Degraders of aromatic compounds upon PAH amendment were shown by the changed extradiol ring-cleavage community structure in soil. The RFLP analysis grouped extradiol dioxygenase marker genes into 17 distinct operational taxonomic units displaying novel phylogenetic clusters of ring-cleavage dioxygenases representing putative catabolic pathways, and the peptide sequences contained conserved amino-acid signatures of extradiol dioxygenases. A branch of major environmental TS cluster was identified as being related to Parvibaculum lavantivorans ring-cleavage dioxygenase. The described structural and functional diversity demonstrated a complex interplay of bacteria in PAH pollution. The findings improve our understanding of rhizoremediation and unveil the extent of uncharacterized enzymes and may benefit bioremediation research by facilitating the development of molecular tools to detect and monitor populations involved in degradative processes.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: In Silico Hhai Fragmentsmentioning

confidence: 99%

Section: Dna Isolation and Pcr Amplificationmentioning

confidence: 99%

See 1 more Smart Citation

High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil

Sipilä

Keskinen²,

Akerman³

et al. 2008

The ISME Journal

View full text Add to dashboard Cite

show abstract

“…The facial triad motif is found in various nonhomologous types of nonheme Fe 2+ -dependent enzymes and commonly serves to control the reactivity of the Fe 2+ site and to activate an aromatic or aliphatic substrate together with dioxygen (9) and is also featured in extradiol-type dioxygenases such as 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) and homoprotocatechuate 2,3-dioxygenase (HPCD) (9,10). Structures of BphC and HPCD in complex with their substrates show that the ortho hydroxyl groups of these catecholic substrates bind as an asymmetric bidentate ligand of Fe 2+ preparing the metal to activate O 2 (11)(12)(13). HGDO may be grouped into a class of extradiol dioxygenases containing the cupin fold and differs from BphC and HPCD by cleaving an aromatic ring with hydroxyl groups in para position, implying a way of Fe 2+ -substrate interaction distinct from the interaction of HPCD and BphC with their Fe 2+ -chelating substrates.…”

mentioning

confidence: 99%

Visualizing the substrate-, superoxo-, alkylperoxo-, and product-bound states at the nonheme Fe(II) site of homogentisate dioxygenase

Jeoung

Bommer

Lin

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Homogentisate 1,2-dioxygenase (HGDO) uses a mononuclear nonheme Fe 2+ to catalyze the oxidative ring cleavage in the degradation of Tyr and Phe by producing maleylacetoacetate from homogentisate (2,5-dihydroxyphenylacetate). Here, we report three crystal structures of HGDO, revealing five different steps in its reaction cycle at 1.7-1.98 Å resolution. The resting state structure displays an octahedral coordination for Fe 2+ with two histidine residues (His331 and His367), a bidentate carboxylate ligand (Glu337), and two water molecules. Homogentisate binds as a monodentate ligand to Fe 2+, and its interaction with Tyr346 invokes the folding of a loop over the active site, effectively shielding it from solvent. Binding of homogentisate is driven by enthalpy and is entropically disfavored as shown by anoxic isothermal titration calorimetry. Three different reaction cycle intermediates have been trapped in different HGDO subunits of a single crystal showing the influence of crystal packing interactions on the course of enzymatic reactions. The observed superoxo:semiquinone-, alkylperoxo-, and product-bound intermediates have been resolved in a crystal grown anoxically with homogentisate, which was subsequently incubated with dioxygen. We demonstrate that, despite different folds, active site architectures, and Fe 2+ coordination, extradiol dioxygenases can proceed through the same principal reaction intermediates to catalyze the O 2 -dependent cleavage of aromatic rings. Thus, convergent evolution of nonhomologous enzymes using the 2-His-1-carboxylate facial triad motif developed different solutions to stabilize closely related intermediates in unlike environments.dioxygen activation | non-heme iron | amino acid degradation | Pseudomonas putida | alkaptonuria H omogentisate (2,5-dihydroxyphenylacetate, HG) is the central metabolite in the degradation pathways of phenylalanine and tyrosine in aerobic organisms ranging from soil bacteria like Pseudomonas putida to man (1, 2). Oxidative ring cleavage is catalyzed by homogentisate 1,2-dioxygenase (HGDO), which incorporates the atoms of molecular oxygen into HG to produce maleylacetoactate (1, 3-6). A deficiency of HGDO is known to cause the autosomal recessive disorder alkaptonuria in humans, the first genetic defect to be recognized as such (6-8). The crystal structure of HGDO from man (HGDO Hs ) revealed that the enzyme belongs to the cupin fold type of nonheme iron-dependent dioxygenases, forming a homohexamer consisting of a dimer of trimers (6). The active site of HGDO Hs employs the 2-His-1-carboxylate facial triad to bind an essential Fe 2+ ion with a distorted square-pyramidal arrangement (6). The facial triad motif is found in various nonhomologous types of nonheme Fe 2+ -dependent enzymes and commonly serves to control the reactivity of the Fe 2+ site and to activate an aromatic or aliphatic substrate together with dioxygen (9) and is also featured in extradiol-type dioxygenases such as 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) and homoprotocatechuate 2,3...

show abstract

“…There is sufficient space for a second monomer in the asymmetric unit, giving a more typical solvent content of 47.4%, but self-rotation and native Patterson maps do not show evidence of a second monomer. We have attempted molecular replacement for phase determination with the programs Phaser v. 1.3 (McCoy, 2007) and MOLREP from the CCP4 program suite (Vagin & Teplyakov, 2010;Collaborative Computational Project, Number 4, 1994) using the structures of reported ASCH-superfamily proteins such as PDB entries 1s04 (G. Liu, R. Xiao, D. K. Sukumaran, T. Acton, G. T. Montelione & T. Szyperski, unpublished work), 1kw8 (Sato et al, 2002), 2eve (Bertonati et al, 2009), 1j2b (Ishitani et al, 2003, 1r3e (Pan et al, 2003) and 2hvy (Li & Ye, 2006) as search models, but have not yet been successful. As mentioned above, their sequence identity is relatively low at less than 15%.…”

Section: Resultsmentioning

confidence: 99%

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of an ASCH domain-containing protein fromZymomonas mobilisZM4

Park

Kim

2011

Acta Crystallogr F Struct Biol Cryst Commun

View full text Add to dashboard Cite

The human activating signal cointegrator 1 (ASC-1) homology (ASCH) domain is frequently observed in many organisms, although its function has not yet been clearly defined. In Zymomonas mobilis ZM4, the ZMO0922 gene encodes a polypeptide that includes an ASCH domain (zmASCH). To provide a better structural background for the probable role of ASCH domain-containing proteins, the ZMO0922 gene was cloned and expressed. The purified protein was crystallized from 30%(w/v) polyethylene glycol 400, 0.1 M cacodylic acid pH 6.5 and 0.2 M lithium sulfate. Diffraction data were collected to 2.1 Å resolution using synchrotron radiation. The crystal belonged to the primitive trigonal space group P3 1 21 or P3 2 21, with unit-cell parameters a = b = 51.67, c = 207.30 Å , = = 90, = 120 . Assuming the presence of one molecule in the asymmetric unit gave a Matthews coefficient of 4.69 Å 3 Da À1, corresponding to a solvent content of 73.7%.

show abstract

Crystal Structures of the Reaction Intermediate and its Homologue of an Extradiol-cleaving Catecholic Dioxygenase

Cited by 105 publications

References 31 publications

High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil

High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil

Visualizing the substrate-, superoxo-, alkylperoxo-, and product-bound states at the nonheme Fe(II) site of homogentisate dioxygenase

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of an ASCH domain-containing protein fromZymomonas mobilisZM4

Contact Info

Product

Resources

About