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Banerjee A, Li J, Molenda MA, Opalade AA, Adhikary A, Brennessel WW, Malkhasian AYS, Jackson TA, Chavez FA. Probing the Mechanism for 2,4'-Dihydroxyacetophenone Dioxygenase Using Biomimetic Iron Complexes. Inorg Chem 2021; 60:7168-7179. [PMID: 33900072 DOI: 10.1021/acs.inorgchem.1c00167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, we report the synthesis and characterization of [Fe(T1Et4iPrIP)(2-OH-AP)(OTf)](OTf) (2), [Fe(T1Et4iPrIP)(2-O-AP)](OTf) (3), and [Fe(T1Et4iPrIP)(DMF)3](OTf)3 (4) (T1Et4iPrIP = tris(1-ethyl-4-isopropyl-imidazolyl)phosphine; 2-OH-AP = 2-hydroxyacetophenone, and 2-O-AP- = monodeprotonated 2-hydroxyacetophenone). Both 2 and 3 serve as model complexes for the enzyme-substrate adduct for the nonheme enzyme 2,4'-dihydroacetophenone (DHAP) dioxygenase or DAD, while 4 serves as a model for the ferric form of DAD. Complexes 2-4 have been characterized by X-ray crystallography which reveals T1Et4iPrIP to bind iron in a tridentate fashion. Complex 2 additionally contains a bidentate 2-OH-AP ligand and a monodentate triflate ligand yielding distorted octahedral geometry, while 3 possesses a bidentate 2-O-AP- ligand and exhibits distorted trigonal bipyramidal geometry (τ = 0.56). Complex 4 displays distorted octahedral geometry with 3 DMF ligands completing the ligand set. The UV-vis spectrum of 2 matches more closely to the DAD-substrate spectrum than 3, and therefore, it is believed that the substrate for DAD is bound in the protonated form. TD-DFT studies indicate that visible absorption bands for 2 and 3 are due to MLCT bands. Complexes 2 and 3 are capable of oxidizing the coordinated substrate mimics in a stoichiometric and catalytic fashion in the presence of O2. Complex 4 does not convert 2-OH-AP to products under the same catalytic conditions; however, it becomes anaerobically reduced in the presence of 2 equiv 2-OH-AP to 2.
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Affiliation(s)
- Atanu Banerjee
- Dr. K. C. Patel R & D Centre, Charotar University of Science and Technology (CHARUSAT), P D Patel Institute of Applied Sciences, 388421 Anand, Gujrat, India
| | - Jia Li
- Department of Chemistry, Oakland University, Rochester, Michigan 48309-4477, United States
| | - Monika A Molenda
- Department of Chemistry, Oakland University, Rochester, Michigan 48309-4477, United States
| | - Adedamola A Opalade
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, Rochester, Michigan 48309-4477, United States
| | - William W Brennessel
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | | | - Timothy A Jackson
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Ferman A Chavez
- Department of Chemistry, Oakland University, Rochester, Michigan 48309-4477, United States
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2
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Roberts KM, Connor GC, Cave CH, Rowe GT, Page CA. The metal- and substrate-dependences of 2,4'-dihydroxyacetophenone dioxygenase. Arch Biochem Biophys 2020; 691:108441. [PMID: 32531315 DOI: 10.1016/j.abb.2020.108441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/11/2022]
Abstract
While the enzyme, 2,4'-dihydroxyacetophenone dioxygenase (DAD), has been known for decades, very little has been characterized of the mechanism of the DAD-catalyzed oxidative cleavage of its reported substrate, 2,4'-dihydroxyacetophenone (DHA). The purpose of this study was to identify the active metal center and to characterize the substrate-dependence of the kinetics of the reaction to lay the foundation for deeper mechanistic investigation. To this, the DAD V1M mutant (bDAD) was overexpressed, purified, and reconstituted with various metal ions. Kinetic assays evaluating the activity of the reconstituted enzyme as well as the substrate- and product-dependences of the reaction kinetics were performed. The results from reconstitution of the apoprotein with a variety of metal ions support the requirement for an Fe3+ center for enzyme activity. Reaction rates showed simple saturation kinetics for DHA with values for kcat and KDHA of 2.4 s-1 and 0.7 μM, respectively, but no significant dependence on the concentration of O2. A low-level inhibition (KI = 1100 μM) by the 4HB product was observed. The results support a minimal kinetic model wherein DHA binds to resting ferric enzyme followed by rapid addition of O2 to yield an intermediate complex that irreversibly collapses to products.
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Affiliation(s)
- Kenneth M Roberts
- Department of Chemistry and Physics, University of South Carolina Aiken, Aiken, SC, 29801, USA.
| | - Gabrielle C Connor
- Department of Chemistry and Physics, University of South Carolina Aiken, Aiken, SC, 29801, USA.
| | - C Haley Cave
- Department of Chemistry and Physics, University of South Carolina Aiken, Aiken, SC, 29801, USA.
| | - Gerard T Rowe
- Department of Chemistry and Physics, University of South Carolina Aiken, Aiken, SC, 29801, USA.
| | - Clinton A Page
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, 29801, USA.
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3
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Banerjee S, Paine TK. Bioinspired iron(II)-β-diketonate and iron(II)-α-hydroxy ketone complexes of a carbanionic N3C ligand: Oxidation of metal center vs C C bond cleavage of co-ligand with dioxygen. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2019.119200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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4
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Elufisan TO, Rodríguez-Luna IC, Oyedara OO, Sánchez-Varela A, Hernández-Mendoza A, Dantán Gonzalez E, Paz-González AD, Muhammad K, Rivera G, Villalobos-Lopez MA, Guo X. The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strain Stenotrophomonas sp. Pemsol isolated from Mexico. PeerJ 2020; 8:e8102. [PMID: 31934497 PMCID: PMC6951288 DOI: 10.7717/peerj.8102] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/25/2019] [Indexed: 11/20/2022] Open
Abstract
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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Affiliation(s)
- Temidayo O Elufisan
- Laboratorio de Biotecnologia Genomica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico.,Science Policy and Innovation Studies (SPIS), National Center for Technology Management Obafemi Awolowo University campus Ile-Ife, Ile-Ife, Osun, Nigeria
| | - Isabel C Rodríguez-Luna
- Laboratorio de Biotecnologia Genomica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
| | | | - Alejandro Sánchez-Varela
- Laboratorio de Biotecnologia Genomica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
| | - Armando Hernández-Mendoza
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos (UAEM), Cuernavaca, Morelos, Mexico
| | - Edgar Dantán Gonzalez
- Laboratorio de Estudios Ecogenómicos (UAEM), Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Alma D Paz-González
- Laboratorio de Biotecnologia Famaceutica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
| | - Kashif Muhammad
- Laboratorio de Biotecnologia Famaceutica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
| | - Gildardo Rivera
- Laboratorio de Biotecnologia Famaceutica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
| | | | - Xianwu Guo
- Laboratorio de Biotecnologia Genomica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
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Leonard DK, Li W, Junge K, Beller M. Improved Bimetallic Cobalt–Manganese Catalysts for Selective Oxidative Cleavage of Morpholine Derivatives. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03476] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- David K. Leonard
- Leibniz Institute for Catalysis at the University of Rostock, Albert-Einstein-Straße 29a, 18059 Rostock, Germany
| | - Wu Li
- Leibniz Institute for Catalysis at the University of Rostock, Albert-Einstein-Straße 29a, 18059 Rostock, Germany
| | - Kathrin Junge
- Leibniz Institute for Catalysis at the University of Rostock, Albert-Einstein-Straße 29a, 18059 Rostock, Germany
| | - Matthias Beller
- Leibniz Institute for Catalysis at the University of Rostock, Albert-Einstein-Straße 29a, 18059 Rostock, Germany
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Manna RN, Malakar T, Jana B, Paul A. Unraveling the Crucial Role of Single Active Water Molecule in the Oxidative Cleavage of Aliphatic C–C Bond of 2,4′-Dihydroxyacetophenone Catalyzed by 2,4′-Dihydroxyacetophenone Dioxygenase Enzyme: A Quantum Mechanics/Molecular Mechanics Investigation. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03201] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rabindra Nath Manna
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Tanmay Malakar
- Raman Center for Atomic, Molecular, and Optical Science, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Ankan Paul
- Raman Center for Atomic, Molecular, and Optical Science, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
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Rigden DJ, Thomas JMH, Simkovic F, Simpkin A, Winn MD, Mayans O, Keegan RM. Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in AMPLE. Acta Crystallogr D Struct Biol 2018; 74:183-193. [PMID: 29533226 PMCID: PMC5947759 DOI: 10.1107/s2059798318002310] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/07/2018] [Indexed: 01/17/2023] Open
Abstract
Molecular replacement (MR) is the predominant route to solution of the phase problem in macromolecular crystallography. Although routine in many cases, it becomes more effortful and often impossible when the available experimental structures typically used as search models are only distantly homologous to the target. Nevertheless, with current powerful MR software, relatively small core structures shared between the target and known structure, of 20-40% of the overall structure for example, can succeed as search models where they can be isolated. Manual sculpting of such small structural cores is rarely attempted and is dependent on the crystallographer's expertise and understanding of the protein family in question. Automated search-model editing has previously been performed on the basis of sequence alignment, in order to eliminate, for example, side chains or loops that are not present in the target, or on the basis of structural features (e.g. solvent accessibility) or crystallographic parameters (e.g. B factors). Here, based on recent work demonstrating a correlation between evolutionary conservation and protein rigidity/packing, novel automated ways to derive edited search models from a given distant homologue over a range of sizes are presented. A variety of structure-based metrics, many readily obtained from online webservers, can be fed to the MR pipeline AMPLE to produce search models that succeed with a set of test cases where expertly manually edited comparators, further processed in diverse ways with MrBUMP, fail. Further significant performance gains result when the structure-based distance geometry method CONCOORD is used to generate ensembles from the distant homologue. To our knowledge, this is the first such approach whereby a single structure is meaningfully transformed into an ensemble for the purposes of MR. Additional cases further demonstrate the advantages of the approach. CONCOORD is freely available and computationally inexpensive, so these novel methods offer readily available new routes to solve difficult MR cases.
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Affiliation(s)
- Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Jens M. H. Thomas
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Felix Simkovic
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Adam Simpkin
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Martyn D. Winn
- Science and Technology Facilities Council, Daresbury Laboratory, Warrington WA4 4AD, England
| | - Olga Mayans
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
| | - Ronan M. Keegan
- Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot OX11 0FA, England
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8
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Bhattacharya S, Rahaman R, Chatterjee S, Paine TK. Aliphatic C-C Bond Cleavage in α-Hydroxy Ketones by a Dioxygen-Derived Nucleophilic Iron-Oxygen Oxidant. Chemistry 2017; 23:3815-3818. [PMID: 28128864 DOI: 10.1002/chem.201605672] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Indexed: 11/06/2022]
Abstract
A nucleophilic iron-oxygen oxidant, formed in situ in the reaction between an iron(II)-benzilate complex and O2 , 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 O2 -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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Affiliation(s)
- Shrabanti Bhattacharya
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, India
| | - Rubina Rahaman
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, India
| | - Sayanti Chatterjee
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, India
| | - Tapan K Paine
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, India
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Zhang S, Wang X, Liu Y. Cleavage mechanism of the aliphatic C–C bond catalyzed by 2,4′-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP: a QM/MM study. Catal Sci Technol 2017. [DOI: 10.1039/c6cy02553f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Calculations suggest that the reactant complex may firstly undergo a triplet–quintet crossing to initiate the reaction and then the subsequent chemistry occurs on the multiple-states surfaces. The key C–C bond cleavage is accompanied by an insertion reaction of oxygen radical.
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Affiliation(s)
- Shujun Zhang
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Xiya Wang
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
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Keegan R, Waterman DG, Hopper DJ, Coates L, Taylor G, Guo J, Coker AR, Erskine PT, Wood SP, Cooper JB. 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. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:933-43. [DOI: 10.1107/s2059798316010433] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/28/2016] [Indexed: 01/27/2023]
Abstract
During efforts to crystallize the enzyme 2,4-dihydroxyacetophenone dioxygenase (DAD) fromAlcaligenessp. 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 usingMOLREPin 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 theMOLREPpeak 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. ABLASTsearch then indicated that the molecule was most probably a phosphate-binding protein fromStenotrophomonas 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 theS. maltophiliaprotein has been refined to anRfactor of 10.15% and anRfreeof 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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Rahaman R, Paria S, Paine TK. Aliphatic C–C Bond Cleavage of α-Hydroxy Ketones by Non-Heme Iron(II) Complexes: Mechanistic Insight into the Reaction Catalyzed by 2,4′-Dihydroxyacetophenone Dioxygenase. Inorg Chem 2015; 54:10576-86. [PMID: 26536067 DOI: 10.1021/acs.inorgchem.5b01235] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rubina Rahaman
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Sayantan Paria
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Tapan Kanti Paine
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
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12
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Guo J, Erskine P, Coker AR, Gor J, Perkins SJ, Wood SP, Cooper JB. Extension of resolution and oligomerization-state studies of 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP. Acta Crystallogr F Struct Biol Commun 2015; 71:1258-63. [PMID: 26457516 PMCID: PMC4601589 DOI: 10.1107/s2053230x15015873] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/25/2015] [Indexed: 11/10/2022] Open
Abstract
The enzyme 2,4'-dihydroxyacetophenone dioxygenase (DAD) catalyses the conversion of 2,4'-dihydroxyacetophenone to 4-hydroxybenzoic acid and formic acid. This enzyme is a very unusual dioxygenase in that it cleaves a C-C bond in a substituent of the aromatic ring rather than within the ring itself. Whilst it has been shown that DAD is a tetramer in solution, the recently solved crystal structure of the Alcaligenes sp. 4HAP enzyme was in fact dimeric rather than tetrameric. Since the use of limited chymotrypsinolysis, which apparently results in removal of the first 20 or so N-terminal residues of DAD, was necessary for crystallization of the protein, it was investigated whether this was responsible for the change in its oligomerization state. Gel-filtration and analytical ultracentrifugation studies were conducted, which confirmed that chymotrypsinolysed DAD has an apparent molecular weight of around 40 kDa, corresponding to a dimer. In contrast, the native enzyme has a molecular weight in the 70-80 kDa region, as expected for the tetramer. The structural basis for tetramerization has been investigated by the use of several docking servers, and the results are remarkably consistent with the tetrameric structure of a homologous cupin protein from Ralstonia eutropha (PDB entry 3ebr).
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Affiliation(s)
- J. Guo
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW2 3PF, England
| | - P. Erskine
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW2 3PF, England
| | - A. R. Coker
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW2 3PF, England
| | - J. Gor
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, England
| | - S. J. Perkins
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, England
| | - S. P. Wood
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW2 3PF, England
| | - J. B. Cooper
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW2 3PF, England
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