Structure of the 2,4′-dihydroxyacetophenone dioxygenase from<i>Alcaligenes</i>sp. 4HAP

Keegan, Ronan; Lebedev, A.A.; Erskine, P.T.; Guo, Jingxu; Wood, Stephen P.; Hopper, David J.; Rigby, Stephen E. J.; Cooper, J.B.

doi:10.1107/s1399004714015053

Cited by 13 publications

(30 citation statements)

References 41 publications

(51 reference statements)

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“…[15] Initialb inding of the a-hydroxyk etone prior to dioxygen activationh as been proposed in the mechanism of the oxidative cleavager eaction by DAD. [16] For CYP17A1, [3,[17][18][19][20][21][22] an iron-peroxide speciesi si mplicated to initiatet he lyase reaction. Only very recently,t he proposed intermediate in the lyase step has been trappeda nd spectroscopically characterizeda sa ni ron-(III)-peroxo-hemiacetals pecies.…”

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confidence: 99%

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Aliphatic C−C Bond Cleavage in α‐Hydroxy Ketones by a Dioxygen‐Derived Nucleophilic Iron–Oxygen Oxidant

Bhattacharya

Rahaman

Chatterjee

et al. 2017

Chemistry A European J

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A nucleophilic iron-oxygen oxidant, formed in situ in the reaction between an iron(II)-benzilate complex and O , oxidatively cleaves the aliphatic C-C bonds of α-hydroxy ketones. In the cleavage reaction, α-hydroxy ketones without any α-C-H bond afford a 1:1 mixture of carboxylic acid and ketone. Isotope labeling studies established that one of the oxygen atoms from dioxygen is incorporated into the carboxylic acid product. Furthermore, the iron(II) complex cleaves an aliphatic C-C bond of 17-α-hydroxyprogesterone affording androstenedione and acetic acid. The O -dependent aliphatic C-C bond cleavage of α-hydroxy ketones containing no α-C-H bond bears similarity to the lyase activity of the heme enzyme, cytochrome P450 17A1 (CYP17A1).

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confidence: 99%

“…GC mass spectrao f: a) androstenedione,and of acetic acid formed in the reaction between 1 and 17a-hydroxyprogesteronewith b)16 O 2 and c)18 O 2 .Inset (c): molecularion peak for acetic acid at m/z 60 ( 16 O) and 62 ( 18 O).…”

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confidence: 99%

Aliphatic C−C Bond Cleavage in α‐Hydroxy Ketones by a Dioxygen‐Derived Nucleophilic Iron–Oxygen Oxidant

Bhattacharya

Rahaman

Chatterjee

et al. 2017

Chemistry A European J

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“…This substitution converts salicylic acid to catechol (Goyal & Zylstra, 1997;Bosch et al, 1999). Two genes, homogentisate 1,2-dioxygenase (PEM_03309) that are involved in the catabolism of aromatic rings (Borowski, Georgiev & Siegbahn, 2005), and 2, 4 dihydroxyacetophenonedioxygenase (PEM_00137), which helps in the cleavage of carbon-carbon bond in a substituent aromatic ring, were also detected (Keegan et al, 2014). The information mentioned above ratifies the capacity of Stenotrophomonas sp.…”

Section: Genetic Basis For the Degradation Of Pah By Stenotrophomonasmentioning

confidence: 68%

The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strainStenotrophomonas sp. Pemsol isolated from Mexico

Elufisan

Rodríguez-Luna

Oyedara

et al. 2020

PeerJ

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Background Stenotrophomonas are ubiquitous gram-negative bacteria, which can survive in a wide range of environments. They can use many substances for their growth and are known to be intrinsically resistant to many antimicrobial agents. They have been tested for biotechnological applications, bioremediation, and production of antimicrobial agents. Method Stenotrophomonas sp. Pemsol was isolated from a crude oil contaminated soil. The capability of this isolate to tolerate and degrade polycyclic aromatic hydrocarbons (PAH) such as anthraquinone, biphenyl, naphthalene, phenanthrene, phenanthridine, and xylene was evaluated in Bushnell Hass medium containing PAHs as the sole carbon sources. The metabolites formed after 30-day degradation of naphthalene by Pemsol were analyzed using Fourier Transform Infra-red Spectroscopic (FTIR), Ultra-Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) and Gas Chromatography-Mass Spectrometry (GC-MS). The genome of Pemsol was also sequenced and analyzed. Results Anthraquinone, biphenyl, naphthalene, phenanthrene, and phenanthridine except xylene can be used as sole carbon sources for Pemsol’s growth in Bushnell Hass medium. The degradation of naphthalene at a concentration of 1 mg/mL within 30 days was tested. A newly formed catechol peak and the disappearance of naphthalene peak detected on the UPLC-MS, and GC-MS analyses spectra respectively confirmed the complete degradation of naphthalene. Pemsol does not produce biosurfactant and neither bio-emulsify PAHs. The whole genome was sequenced and assembled into one scaffold with a length of 4,373,402 bp. A total of 145 genes involved in the degradation of PAHs were found in its genome, some of which are Pemsol-specific as compared with other 11 Stenotrophomonas genomes. Most specific genes are located on the genomic islands. Stenotrophomonas sp. Pemsol’s possession of few genes that are associated with bio-emulsification gives the genetic basis for its inability to bio-emulsify PAH. A possible degradation pathway for naphthalene in Pemsol was proposed following the analysis of Pemsol’s genome. ANI and GGDH analysis indicated that Pemsol is likely a new species of Stenotrophomonas. It is the first report on a complete genome sequence analysis of a PAH-degrading Stenotrophomonas. Stenotrophomonas sp. Pemsol possesses features that make it a good bacterium for genetic engineering and will be an excellent tool for the remediation of crude oil or PAH-contaminated soil.

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“…Use of the MATT-PROB server (Kantardjieff & Rupp, 2003) indicated that there were likely to be two molecules of DAD (which are approximately 20 kDa each) in the asymmetric unit. However, attempts at molecular replacement with various search models which had sequence homology to DAD failed to yield a solution, and when the structure of DAD was solved in a different crystal form (Beaven et al, 2014;Keegan et al, 2014) this also did not provide a convincing solution with the 1.1 Å resolution data set.…”

Section: Data Processingmentioning

confidence: 99%

The 1.1 Å resolution structure of a periplasmic phosphate-binding protein fromStenotrophomonas maltophilia: a crystallization contaminant identified by molecular replacement using the entire Protein Data Bank

Keegan

Hopper

Coates

et al. 2016

Acta Crystallogr D Struct Biol

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During efforts to crystallize the enzyme 2,4-dihydroxyacetophenone dioxygenase (DAD) from Alcaligenes sp. 4HAP, a small number of strongly diffracting protein crystals were obtained after two years of crystal growth in one condition. The crystals diffracted synchrotron radiation to almost 1.0 Å resolution and were, until recently, assumed to be formed by the DAD protein. However, when another crystal form of this enzyme was eventually solved at lower resolution, molecular replacement using this new structure as the search model did not give a convincing solution with the original atomic resolution data set. Hence, it was considered that these crystals might have arisen from a protein impurity, although molecular replacement using the structures of common crystallization contaminants as search models again failed. A script to perform molecular replacement using MOLREP in which the first chain of every structure in the PDB was used as a search model was run on a multi-core cluster. This identified a number of prokaryotic phosphate-binding proteins as scoring highly in the MOLREP peak lists. Calculation of an electron-density map at 1.1 Å resolution based on the solution obtained with PDB entry 2q9t allowed most of the amino acids to be identified visually and built into the model. A BLAST search then indicated that the molecule was most probably a phosphate-binding protein from Stenotrophomonas maltophilia (UniProt ID B4SL31; gene ID Smal_2208), and fitting of the corresponding sequence to the atomic resolution map fully corroborated this. Proteins in this family have been linked to the virulence of antibiotic-resistant strains of pathogenic bacteria and with biofilm formation. The structure of the S. maltophilia protein has been refined to an R factor of 10.15% and an Rfree of 12.46% at 1.1 Å resolution. The molecule adopts the type II periplasmic binding protein (PBP) fold with a number of extensively elaborated loop regions. A fully dehydrated phosphate anion is bound tightly between the two domains of the protein and interacts with conserved residues and a number of helix dipoles.

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Structure of the 2,4′-dihydroxyacetophenone dioxygenase fromAlcaligenessp. 4HAP

Cited by 13 publications

References 41 publications

Aliphatic C−C Bond Cleavage in α‐Hydroxy Ketones by a Dioxygen‐Derived Nucleophilic Iron–Oxygen Oxidant

Aliphatic C−C Bond Cleavage in α‐Hydroxy Ketones by a Dioxygen‐Derived Nucleophilic Iron–Oxygen Oxidant

The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strainStenotrophomonas sp. Pemsol isolated from Mexico

The 1.1 Å resolution structure of a periplasmic phosphate-binding protein fromStenotrophomonas maltophilia: a crystallization contaminant identified by molecular replacement using the entire Protein Data Bank

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