1
|
Koehn EM, Lang A, Flores A, Lambert C, Klinman J. Replacement of Tyrosines by Unnatural Amino Acid Aminophenylalanine Leads to Metal-Mediated Aniline Free Radical Formation in a Copper Amine Oxidase. ACS Chem Biol 2024; 19:1525-1532. [PMID: 38889186 DOI: 10.1021/acschembio.4c00198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Copper amine oxidases (CAOs) catalyze the oxidative deamination of primary amines to aldehyde, ammonia, and hydrogen peroxide as products and are widely distributed in bacteria, plants, and eukaryotes. These enzymes initiate the single turnover, post-translational conversion of an active site tyrosine to the redox cofactor 2,4,5-trihydroxyphenylalanine quinone (TPQ), subsequently employing TPQ to catalyze steady-state amine oxidation. The mechanisms of TPQ biogenesis and steady-state amine oxidation have been studied extensively, with consensus mechanisms proposed for both reactions. One unresolved issue has been whether the Cu2+ center must undergo formal reduction to Cu1+ in the course of the reaction. Herein, we investigate the properties of the active site of a yeast (Hansenula polymorpha) amine oxidase (HPAO) that has undergone site-specific insertion of a para-aminophenylalanine (pAF) into the position of either the precursor tyrosine to TPQ (Y405) or the two strictly conserved neighboring tyrosines (Y305 and Y407). While our original intention was to interrogate cofactor biogenesis using a precursor unnatural amino acid (UAA) of altered redox potential and pKa, we instead observe an unanticipated reaction assigned to an intramolecular electron transfer from pAF to the active site copper ion. We establish the generality of the observed active site chemistry using exogenously added, aniline-containing substrates under conditions that prevent side chain amine oxidation. The results support previous proposals that the activation of the TPQ precursor occurs in the absence of a formal valence change at the active site copper site. The described reaction of pAFs with the active site redox Cu2+ center of HPAO provides a prototype for either the engineering of the enzymatic oxidation of exogenous anilines or the insertion of site-specific free radical probes within proteins.
Collapse
Affiliation(s)
- Eric M Koehn
- Department of Chemistry and California Institute for Quantitative Biosciences, University of California-Berkeley, Berkeley, California 94720-3220, United States
| | - Albert Lang
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California 94720-3220, United States
| | - Allison Flores
- Department of Chemistry and California Institute for Quantitative Biosciences, University of California-Berkeley, Berkeley, California 94720-3220, United States
| | - Claudia Lambert
- Department of Chemistry and California Institute for Quantitative Biosciences, University of California-Berkeley, Berkeley, California 94720-3220, United States
| | - Judith Klinman
- Department of Chemistry and California Institute for Quantitative Biosciences, University of California-Berkeley, Berkeley, California 94720-3220, United States
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California 94720-3220, United States
| |
Collapse
|
2
|
Salman BI, Hassan AI, Saraya RE, Ibrahim AE, Mohammed BS, Batakoushy HA, El Deeb S, Hassan YF. Development of cysteine-doped MnO 2 quantum dots for spectrofluorimetric estimation of copper: applications in different matrices. Anal Bioanal Chem 2023; 415:5529-5538. [PMID: 37432444 PMCID: PMC10444647 DOI: 10.1007/s00216-023-04827-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/01/2023] [Accepted: 06/19/2023] [Indexed: 07/12/2023]
Abstract
Copper (Cu) plays a role in maintaining healthy nerve cells and the immune system. Osteoporosis is a high-risk factor for Cu deficiency. In the proposed research, unique green, fluorescent cysteine-doped MnO2 quantum dots (Cys@MnO2 QDs) were synthesized and assessed for the determination of Cu in different food and hair samples. The developed quantum dots were synthesized with the help of cysteine using a straightforward ultrasonic approach to create 3D fluorescent Cys@MnO2 QDs. The resulting QDs' morphological and optical characteristics were carefully characterized. By adding Cu ions, the intensity of fluorescence for the produced Cys@MnO2 QDs was found to be dramatically reduced. Additionally, the applicability of Cys@MnO2 QDs as a new luminous nanoprobe was found to be strengthened by the quenching effect grounded on the Cu-S bonding. The concentrations of Cu2+ ions were estimated within the range of 0.06 to 7.00 µg mL-1, with limit of quantitation equal to 33.33 ng mL-1 and detection limit equal to 10.97 ng mL-1. The Cys@MnO2 QD technique was applied successfully for the quantification of Cu in a variety of foods, including chicken meat, turkey, and tinned fish, as well as in human hair samples. The chance that this novel technique could be a useful tool for figuring out the amount of cysteine in bio-samples is increased by the sensing system's remarkable advantages, which include being rapid, simple, and economical.
Collapse
Affiliation(s)
- Baher I Salman
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut, 71524, Egypt
| | - Ahmed I Hassan
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut, 71524, Egypt
| | - Roshdy E Saraya
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Port Said University, Port Said, 42511, Egypt
| | - Adel Ehab Ibrahim
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Port Said University, Port Said, 42511, Egypt
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al Mauz, P.O. Box 33, Nizwa, 616, Sultanate of Oman
| | - Bassam Shaaban Mohammed
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Menoufia University, Shibin-Elkom, 32511, Egypt
| | - Hany A Batakoushy
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Menoufia University, Shibin-Elkom, 32511, Egypt
| | - Sami El Deeb
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al Mauz, P.O. Box 33, Nizwa, 616, Sultanate of Oman.
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universitaet Braunschweig, 38106, Braunschweig, Germany.
| | - Yasser F Hassan
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut, 71524, Egypt
| |
Collapse
|
3
|
Zhu B, Du Z, Dai Y, Kitaguchi T, Behrens S, Seelig B. Nanodroplet-Based Reagent Delivery into Water-in-Fluorinated-Oil Droplets. BIOSENSORS 2023; 13:768. [PMID: 37622854 PMCID: PMC10452409 DOI: 10.3390/bios13080768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023]
Abstract
In vitro compartmentalization (IVC) is a technique for generating water-in-oil microdroplets to establish the genotype (DNA information)-phenotype (biomolecule function) linkage required by many biological applications. Recently, fluorinated oils have become more widely used for making microdroplets due to their better biocompatibility. However, it is difficult to perform multi-step reactions requiring the addition of reagents in water-in-fluorinated-oil microdroplets. On-chip droplet manipulation is usually used for such purposes, but it may encounter some technical issues such as low throughput or time delay of reagent delivery into different microdroplets. Hence, to overcome the above issues, we demonstrated a nanodroplet-based approach for the delivery of copper ions and middle-sized peptide molecules (human p53 peptide, 2 kDa). We confirmed the ion delivery by microscopic inspection of crystal formation inside the microdroplet, and confirmed the peptide delivery using a fluorescent immunosensor. We believe that this nanodroplet-based delivery method is a promising approach to achieving precise control for a broad range of fluorocarbon IVC-based biological applications, including molecular evolution, cell factory engineering, digital nucleic acid detection, or drug screening.
Collapse
Affiliation(s)
- Bo Zhu
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Zhe Du
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
- Center for Environmental Health Risk Assessment and Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yancen Dai
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Tetsuya Kitaguchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Sebastian Behrens
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
| |
Collapse
|
4
|
Khan W, El-Shehawi AM, Ali F, Ali M, Alqurashi M, Althaqafi MM, Alharthi SB. A Genome-Wide Identification and Expression Pattern of LMCO Gene Family from Turnip ( Brassica rapa L.) under Various Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091904. [PMID: 37176963 PMCID: PMC10180887 DOI: 10.3390/plants12091904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/29/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023]
Abstract
Laccase-like multi-copper oxidases (LMCOs) are a group of enzymes involved in the oxidation of numerous substrates. Recently, these enzymes have become extremely popular due to their practical applications in various fields of biology. LMCOs generally oxidize various substrates by linking four-electron reduction of the final acceptor, molecular oxygen (O2), to water. Multi-copper oxidases related to laccase are extensively distributed as multi-gene families in the genome sequences of higher plants. The current study thoroughly investigated the LMCO gene family (Br-Lac) and its expression pattern under various abiotic stresses in B. rapa L. A total of 18 Br-Lac gene family members located on five different chromosomes were identified. Phylogenetic analysis classified the documented Br-Lac genes into seven groups: Group-I (four genes), Group-II (nine genes), Group-III (eight genes), Group-IV (four genes), Group-V (six genes), and Group-VI and Group-VII (one gene each). The key features of gene structure and responsive motifs shared the utmost resemblance within the same groups. Additionally, a divergence study also assessed the evolutionary features of Br-Lac genes. The anticipated period of divergence ranged from 12.365 to 39.250 MYA (million years ago). We also identified the pivotal role of the 18 documented members of the LMCO (Br-lac) gene family using quantitative real-time qRT-PCR. Br-Lac-6, Br-Lac-7, Br-Lac-8, Br-Lac-16, Br-Lac-17, and Br-Lac-22 responded positively to abiotic stresses (i.e., drought, heat, and salinity). These findings set the stage for the functional diversity of the LMCO genes in B. rapa.
Collapse
Affiliation(s)
- Waqar Khan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Ahmed M El-Shehawi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Fayaz Ali
- Department of Botany, Shaheed Benazir Bhutto University, Sheringal, Dir Upper P.O. Box 18050, Pakistan
| | - Murad Ali
- Department of Botany, Hazara University Mansehra, Mansehra P.O. Box 21300, Pakistan
| | - Mohammed Alqurashi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Mohammed M Althaqafi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Siraj B Alharthi
- Department of Biological Sciences, King Abdulaziz University, P.O. Box 16834, Jeddah 21474, Saudi Arabia
| |
Collapse
|
5
|
Ziółkowska A, Witwicki M. Understanding the Exchange Interaction between Paramagnetic Metal Ions and Radical Ligands: DFT and Ab Initio Study on Semiquinonato Cu(II) Complexes. Int J Mol Sci 2023; 24:ijms24044001. [PMID: 36835412 PMCID: PMC9959031 DOI: 10.3390/ijms24044001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
The exchange coupling, represented by the J parameter, is of tremendous importance in understanding the reactivity and magnetic behavior of open-shell molecular systems. In the past, it was the subject of theoretical investigations, but these studies are mostly limited to the interaction between metallic centers. The exchange coupling between paramagnetic metal ions and radical ligands has hitherto received scant attention in theoretical studies, and thus the understanding of the factors governing this interaction is lacking. In this paper, we use DFT, CASSCF, CASSCF/NEVPT2, and DDCI3 methods to provide insight into exchange interaction in semiquinonato copper(II) complexes. Our primary objective is to identify structural features that affect this magnetic interaction. We demonstrate that the magnetic character of Cu(II)-semiquinone complexes are mainly determined by the relative position of the semiquinone ligand to the Cu(II) ion. The results can support the experimental interpretation of magnetic data for similar systems and can be used for the in-silico design of magnetic complexes with radical ligands.
Collapse
Affiliation(s)
- Aleksandra Ziółkowska
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Maciej Witwicki
- Faculty of Chemistry, Wroclaw University, F. Joliot-Curie 14, 50-283 Wroclaw, Poland
- Correspondence:
| |
Collapse
|
6
|
Meier AA, Kuczera K, Mure M. A 3D-Predicted Structure of the Amine Oxidase Domain of Lysyl Oxidase-Like 2. Int J Mol Sci 2022; 23:13385. [PMID: 36362176 PMCID: PMC9659206 DOI: 10.3390/ijms232113385] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 07/30/2023] Open
Abstract
Lysyl oxidase-like 2 (LOXL2) has been recognized as an attractive drug target for anti-fibrotic and anti-tumor therapies. However, the structure-based drug design of LOXL2 has been very challenging due to the lack of structural information of the catalytically-competent LOXL2. In this study; we generated a 3D-predicted structure of the C-terminal amine oxidase domain of LOXL2 containing the lysine tyrosylquinone (LTQ) cofactor from the 2.4Å crystal structure of the Zn2+-bound precursor (lacking LTQ; PDB:5ZE3); this was achieved by molecular modeling and molecular dynamics simulation based on our solution studies of a mature LOXL2 that is inhibited by 2-hydrazinopyridine. The overall structures of the 3D-modeled mature LOXL2 and the Zn2+-bound precursor are very similar (RMSD = 1.070Å), and disulfide bonds are conserved. The major difference of the mature and the precursor LOXL2 is the secondary structure of the pentapeptide (His652-Lys653-Ala654-Ser655-Phe656) containing Lys653 (the precursor residue of the LTQ cofactor). We anticipate that this peptide is flexible in solution to accommodate the conformation that enables the LTQ cofactor formation as opposed to the β-sheet observed in 5ZE3. We discuss the active site environment surrounding LTQ and Cu2+ of the 3D-predicted structure.
Collapse
Affiliation(s)
- Alex A. Meier
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
| | - Krzysztof Kuczera
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Minae Mure
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
| |
Collapse
|
7
|
Murakawa T, Kurihara K, Adachi M, Kusaka K, Tanizawa K, Okajima T. Re-evaluation of protein neutron crystallography with and without X-ray/neutron joint refinement. IUCRJ 2022; 9:342-348. [PMID: 35546796 PMCID: PMC9067118 DOI: 10.1107/s2052252522003657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Protein neutron crystallography is a powerful technique to determine the positions of H atoms, providing crucial biochemical information such as the protonation states of catalytic groups and the geometry of hydrogen bonds. Recently, the crystal structure of a bacterial copper amine oxidase was determined by joint refinement using X-ray and neutron diffraction data sets at resolutions of 1.14 and 1.72 Å, respectively [Murakawa et al. (2020 ▸). Proc. Natl Acad. Sci. USA, 117, 10818-10824]. While joint refinement is effective for the determination of the accurate positions of heavy atoms on the basis of the electron density, the structural information on light atoms (hydrogen and deuterium) derived from the neutron diffraction data might be affected by the X-ray data. To unravel the information included in the neutron diffraction data, the structure determination was conducted again using only the neutron diffraction data at 1.72 Å resolution and the results were compared with those obtained in the previous study. Most H and D atoms were identified at essentially the same positions in both the neutron-only and the X-ray/neutron joint refinements. Nevertheless, neutron-only refinement was found to be less effective than joint refinement in providing very accurate heavy-atom coordinates that lead to significant improvement of the neutron scattering length density map, especially for the active-site cofactor. Consequently, it was confirmed that X-ray/neutron joint refinement is crucial for determination of the real chemical structure of the catalytic site of the enzyme.
Collapse
Affiliation(s)
- Takeshi Murakawa
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan
| | - Kazuo Kurihara
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Motoyasu Adachi
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Katsuyuki Tanizawa
- Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Toshihide Okajima
- Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| |
Collapse
|
8
|
Shoji M, Murakawa T, Nakanishi S, Boero M, Shigeta Y, Hayashi H, Okajima T. Molecular mechanism of a large conformational change of the quinone cofactor in the semiquinone intermediate of bacterial copper amine oxidase. Chem Sci 2022; 13:10923-10938. [PMID: 36320691 PMCID: PMC9491219 DOI: 10.1039/d2sc01356h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/16/2022] [Indexed: 11/21/2022] Open
Abstract
Copper amine oxidase from Arthrobacter globiformis (AGAO) catalyses the oxidative deamination of primary amines via a large conformational change of a topaquinone (TPQ) cofactor during the semiquinone formation step. This conformational change of TPQ occurs in the presence of strong hydrogen bonds and neighboring bulky amino acids, especially the conserved Asn381, which restricts TPQ conformational changes over the catalytic cycle. Whether such a semiquinone intermediate is catalytically active or inert has been a matter of debate in copper amine oxidases. Here, we show that the reaction rate of the Asn381Ala mutant decreases 160-fold, and the X-ray crystal structures of the mutant reveals a TPQ-flipped conformation in both the oxidized and reduced states, preceding semiquinone formation. Our hybrid quantum mechanics/molecular mechanics (QM/MM) simulations show that the TPQ conformational change is realized through the sequential steps of the TPQ ring-rotation and slide. We determine that the bulky side chain of Asn381 hinders the undesired TPQ ring-rotation in the oxidized form, favoring the TPQ ring-rotation in reduced TPQ by a further stabilization leading to the TPQ semiquinone form. The acquired conformational flexibility of TPQ semiquinone promotes a high reactivity of Cu(i) to O2, suggesting that the semiquinone form is catalytically active for the subsequent oxidative half-reaction in AGAO. The ingenious molecular mechanism exerted by TPQ to achieve the “state-specific” reaction sheds new light on a drastic environmental transformation around the catalytic center. The large conformational change of topaquinone in bacterial copper amine oxidase occurs through the TPQ ring rotation and slide, which are essential to stabilize the semiquinone form.![]()
Collapse
Affiliation(s)
- Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba 1-1-1 Tennodai Tsukuba 305-8577 Ibaraki Japan
- JST-PRESTO 4-1-8 Honcho Kawaguchi 332-0012 Saitama Japan
| | - Takeshi Murakawa
- Department of Biochemistry, Osaka Medical and Pharmaceutical University 2-7 Daigakumachi Takatsuki 569-8686 Osaka Japan
| | - Shota Nakanishi
- Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka Ibaraki 567-0047 Osaka Japan
| | - Mauro Boero
- University of Strasbourg, Institut de Physique et Chimie des Matériaux de Strasbourg, CNRS, UMR 7504 23 rue du Loess F-67034 France
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba 1-1-1 Tennodai Tsukuba 305-8577 Ibaraki Japan
| | - Hideyuki Hayashi
- Department of Chemistry, Osaka Medical and Pharmaceutical University 2-7 Daigakumachi Takatsuki 569-8686 Osaka Japan
| | - Toshihide Okajima
- Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka Ibaraki 567-0047 Osaka Japan
- Department of Chemistry, Osaka Medical and Pharmaceutical University 2-7 Daigakumachi Takatsuki 569-8686 Osaka Japan
| |
Collapse
|
9
|
Murakawa T, Suzuki M, Arima T, Sugahara M, Tanaka T, Tanaka R, Iwata S, Nango E, Tono K, Hayashi H, Fukui K, Yano T, Tanizawa K, Okajima T. Microcrystal preparation for serial femtosecond X-ray crystallography of bacterial copper amine oxidase. Acta Crystallogr F Struct Biol Commun 2021; 77:356-363. [PMID: 34605440 PMCID: PMC8488853 DOI: 10.1107/s2053230x21008967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/28/2021] [Indexed: 11/10/2022] Open
Abstract
Recent advances in serial femtosecond X-ray crystallography (SFX) using X-ray free-electron lasers have paved the way for determining radiation-damage-free protein structures under nonfreezing conditions. However, the large-scale preparation of high-quality microcrystals of uniform size is a prerequisite for SFX, and this has been a barrier to its widespread application. Here, a convenient method for preparing high-quality microcrystals of a bacterial quinoprotein enzyme, copper amine oxidase from Arthrobacter globiformis, is reported. The method consists of the mechanical crushing of large crystals (5-15 mm3), seeding the crushed crystals into the enzyme solution and standing for 1 h at an ambient temperature of ∼26°C, leading to the rapid formation of microcrystals with a uniform size of 3-5 µm. The microcrystals diffracted X-rays to a resolution beyond 2.0 Å in SFX measurements at the SPring-8 Angstrom Compact Free Electron Laser facility. The damage-free structure determined at 2.2 Å resolution was essentially identical to that determined previously by cryogenic crystallography using synchrotron X-ray radiation.
Collapse
Affiliation(s)
- Takeshi Murakawa
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan
| | - Mamoru Suzuki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshi Arima
- SPring-8 Center, RIKEN, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Michihiro Sugahara
- SPring-8 Center, RIKEN, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Tomoyuki Tanaka
- SPring-8 Center, RIKEN, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Rie Tanaka
- SPring-8 Center, RIKEN, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - So Iwata
- SPring-8 Center, RIKEN, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Eriko Nango
- SPring-8 Center, RIKEN, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Kensuke Tono
- SPring-8 Center, RIKEN, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Hideyuki Hayashi
- Department of Chemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan
| | - Kenji Fukui
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan
| | - Takato Yano
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan
| | - Katsuyuki Tanizawa
- Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Toshihide Okajima
- Department of Chemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan
- Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| |
Collapse
|
10
|
Schröder GC, Meilleur F. Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography. Acta Crystallogr D Struct Biol 2021; 77:1251-1269. [PMID: 34605429 PMCID: PMC8489226 DOI: 10.1107/s2059798321009025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/31/2021] [Indexed: 11/11/2022] Open
Abstract
Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.
Collapse
Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| |
Collapse
|
11
|
Russell H, Stewart R, Prior C, Oganesyan VS, Gaule TG, Lovett JE. DEER and RIDME Measurements of the Nitroxide-Spin Labelled Copper-Bound Amine Oxidase Homodimer from Arthrobacter Globiformis. APPLIED MAGNETIC RESONANCE 2021; 52:995-1015. [PMID: 34720439 PMCID: PMC8550341 DOI: 10.1007/s00723-021-01321-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/23/2021] [Accepted: 03/10/2021] [Indexed: 06/13/2023]
Abstract
In the study of biological structures, pulse dipolar spectroscopy (PDS) is used to elucidate spin-spin distances at nanometre-scale by measuring dipole-dipole interactions between paramagnetic centres. The PDS methods of Double Electron Electron Resonance (DEER) and Relaxation Induced Dipolar Modulation Enhancement (RIDME) are employed, and their results compared, for the measurement of the dipolar coupling between nitroxide spin labels and copper-II (Cu(II)) paramagnetic centres within the copper amine oxidase from Arthrobacter globiformis (AGAO). The distance distribution results obtained indicate that two distinct distances can be measured, with the longer of these at c.a. 5 nm. Conditions for optimising the RIDME experiment such that it may outperform DEER for these long distances are discussed. Modelling methods are used to show that the distances obtained after data analysis are consistent with the structure of AGAO. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s00723-021-01321-6.
Collapse
Affiliation(s)
- Hannah Russell
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, St Andrews, KY16 9SS UK
| | - Rachel Stewart
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, St Andrews, KY16 9SS UK
| | | | | | - Thembaninkosi G. Gaule
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Janet E. Lovett
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, St Andrews, KY16 9SS UK
| |
Collapse
|
12
|
Shoji M, Murakawa T, Boero M, Shigeta Y, Hayashi H, Okajima T. Unique protonation states of aspartate and topaquinone in the active site of copper amine oxidase. RSC Adv 2020; 10:38631-38639. [PMID: 35517562 PMCID: PMC9057271 DOI: 10.1039/d0ra06365g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/13/2020] [Indexed: 01/31/2023] Open
Abstract
The oxidative deamination of biogenic amines, crucial in the metabolism of a wealth of living organisms, is catalyzed by copper amine oxidases (CAOs). In this work, on the ground of accurate molecular modeling, we provide a clear insight into the unique protonation states of the key catalytic aspartate residue Asp298 and the prosthetic group of topaquinone (TPQ) in the CAO of Arthrobacter globiformis (AGAO). This provides both extensions and complementary information to the crystal structure determined by our recent neutron diffraction (ND) experiment. The hybrid quantum mechanics/molecular mechanics (QM/MM) simulations suggest that the ND structure closely resembles a state in which Asp298 is protonated and the TPQ takes an enolate form. The TPQ keto form can coexist in the fully protonated state. The energetic and structural analyses indicate that the active site structure of the AGAO crystal is not a single state but rather a mixture of the different protonation and conformational states identified in this work. Copper amine oxidases catalyze the oxidative deamination of biogenic amines. We investigated the unique protonation states in the active site using first-principle calculations.![]()
Collapse
Affiliation(s)
- Mitsuo Shoji
- Center for Computational Sciences
- University of Tsukuba
- Tsukuba
- Japan
- JST-PRESTO
| | | | - Mauro Boero
- University of Strasbourg
- Institut de Physique et Chimie des Matériaux de Strasbourg
- CNRS
- UMR 7504
- France
| | - Yasuteru Shigeta
- Center for Computational Sciences
- University of Tsukuba
- Tsukuba
- Japan
| | | | - Toshihide Okajima
- Department of Chemistry
- Osaka Medical College
- Takatsuki
- Japan
- Institute of Scientific and Industrial Research
| |
Collapse
|
13
|
Dey S, Maity S, Pal K, Jana K, Sinha C. The oxidative dehydrogenation of a coumarinyl scaffold with copper ion and metal ion detection in human liver cancer cells (HepG2). Dalton Trans 2019; 48:17818-17830. [PMID: 31774094 DOI: 10.1039/c9dt03870a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
An unsymmetrical o-phenylenediamine derivative, L (7-hydroxy-4-methyl-8-(1-(phenyl- (pyridin-2-yl)methyl)-1H-benzo[d]imidazol-2-yl)-2H-chromen-2-one), has been synthesized from (E)-N1-(phenyl(pyridine-2-yl)methylene)benzene-1,2-diamine with 7-hydroxy-4-methyl-2-oxo-2H-chromene-8-carbaldehyde and characterized by X-ray, IR, 1H NMR and ESI-MS spectral analyses. The X-ray structure shows L as a cyclic benzimidazole derivative, but it undergoes ring-opening upon reaction with transition metal ions. L is non-emissive in 9 : 1 (v/v) EtOH/H2O (HEPES buffer, pH 7.4) but becomes highly fluorescent upon Zn2+ coordination, and the emissive Zn(ii) complex undergoes transmetallation in the presence of Cu2+ ions specifically, followed by amine to imine oxidation, i.e. an oxidative dehydrogenation (OD) reaction -(2e + 2H+) occurs. The transmetallation of Zn2+ from the complex by Cu2+ (CuCl2) separated the non-emissive X-ray diffractable crystal of [Cu(L'')Cl] (L'' = amine oxidized form of L). A square pyramidal [Cu(L'')][ClO4] complex was also isolated from the reaction of L with Cu(CH3CN)4(ClO4) in the presence of air, and in this complex the amine is also oxidized to the imine. Here, copper ions in the presence of air play an important role in the OD reaction of L as determined by EPR and cyclic voltammetry studies. The ligand, L, is used for Zn2+ ion recovery from a municipally supplied water sample. A paper strip detection kit for Zn2+ and Cu2+ is designed using L. The ligand is also used for intracellular Zn2+ detection in a human liver cancer cell line (HepG2).
Collapse
Affiliation(s)
- Sunanda Dey
- Department of Chemistry, Jadavpur University, Kolkata-700032, India.
| | - Suvendu Maity
- Department of Chemistry, Jadavpur University, Kolkata-700032, India.
| | - Kunal Pal
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata-700032, India and Division of Molecular Medicine, Bose Institute, Kolkata-700056, India
| | - Kuladip Jana
- Division of Molecular Medicine, Bose Institute, Kolkata-700056, India
| | | |
Collapse
|
14
|
Chan JC, Paice M, Zhang X. Enzymatic Oxidation of Lignin: Challenges and Barriers Toward Practical Applications. ChemCatChem 2019. [DOI: 10.1002/cctc.201901480] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jou C. Chan
- Voiland School of Chemical Engineering and Bioengineering Washington State University 2710 Crimson Way Richland WA-99354 USA
| | - Michael Paice
- FPInnovations Pulp Paper & Bioproducts 2665 East Mall Vancouver BC V6T 1Z4 Canada
| | - Xiao Zhang
- Voiland School of Chemical Engineering and Bioengineering Washington State University 2710 Crimson Way Richland WA-99354 USA
- Pacific Northwest National Laboratory 520 Battelle Boulevard P.O. Box 999, MSIN P8-60 Richland WA-99352 USA
| |
Collapse
|
15
|
Active-site environment of Cu bound amyloid β and amylin peptides. J Biol Inorg Chem 2019; 24:1245-1259. [DOI: 10.1007/s00775-019-01724-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/05/2019] [Indexed: 01/09/2023]
|
16
|
In crystallo thermodynamic analysis of conformational change of the topaquinone cofactor in bacterial copper amine oxidase. Proc Natl Acad Sci U S A 2018; 116:135-140. [PMID: 30563857 DOI: 10.1073/pnas.1811837116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
In the catalytic reaction of copper amine oxidase, the protein-derived redox cofactor topaquinone (TPQ) is reduced by an amine substrate to an aminoresorcinol form (TPQamr), which is in equilibrium with a semiquinone radical (TPQsq). The transition from TPQamr to TPQsq is an endothermic process, accompanied by a significant conformational change of the cofactor. We employed the humid air and glue-coating (HAG) method to capture the equilibrium mixture of TPQamr and TPQsq in noncryocooled crystals of the enzyme from Arthrobacter globiformis and found that the equilibrium shifts more toward TPQsq in crystals than in solution. Thermodynamic analyses of the temperature-dependent equilibrium also revealed that the transition to TPQsq is entropy-driven both in crystals and in solution, giving the thermodynamic parameters that led to experimental determination of the crystal packing effect. Furthermore, we demonstrate that the binding of product aldehyde to the hydrophobic pocket in the active site produces various equilibrium states among two forms of the product Schiff-base, TPQamr, and TPQsq, in a pH-dependent manner. The temperature-controlled HAG method provides a technique for thermodynamic analysis of conformational changes occurring in protein crystals that are hardly scrutinized by conventional cryogenic X-ray crystallography.
Collapse
|
17
|
The Pseudoalteromonas luteoviolacea L-amino Acid Oxidase with Antimicrobial Activity Is a Flavoenzyme. Mar Drugs 2018; 16:md16120499. [PMID: 30545033 PMCID: PMC6316408 DOI: 10.3390/md16120499] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 11/30/2018] [Accepted: 12/07/2018] [Indexed: 12/11/2022] Open
Abstract
The marine environment is a rich source of antimicrobial compounds with promising pharmaceutical and biotechnological applications. The Pseudoalteromonas genus harbors one of the highest proportions of bacterial species producing antimicrobial molecules. For decades, the presence of proteins with L-amino acid oxidase (LAAO) and antimicrobial activity in Pseudoalteromonas luteoviolacea has been known. Here, we present for the first time the identification, cloning, characterization and phylogenetic analysis of Pl-LAAO, the enzyme responsible for both LAAO and antimicrobial activity in P. luteoviolacea strain CPMOR-2. Pl-LAAO is a flavoprotein of a broad substrate range, in which the hydrogen peroxide generated in the LAAO reaction is responsible for the antimicrobial activity. So far, no protein with a sequence similarity to Pl-LAAO has been cloned or characterized, with this being the first report on a flavin adenine dinucleotide (FAD)-containing LAAO with antimicrobial activity from a marine microorganism. Our results revealed that 20.4% of the sequenced Pseudoalteromonas strains (specifically, 66.6% of P. luteoviolacea strains) contain Pl-laao similar genes, which constitutes a well-defined phylogenetic group. In summary, this work provides insights into the biological significance of antimicrobial LAAOs in the Pseudoalteromonas genus and shows an effective approach for the detection of novel LAAOs, whose study may be useful for biotechnological applications.
Collapse
|
18
|
Oke M, Agbalajobi R, Osifeso M, Muhammad B, Lawal H, Mai M, Adegunle Q. Design and implementation of structural bioinformatics projects for biological sciences undergraduate students. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 46:547-554. [PMID: 30369034 DOI: 10.1002/bmb.21169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/21/2018] [Accepted: 09/03/2018] [Indexed: 06/08/2023]
Abstract
Contemporary biology is currently undergoing a revolution, driven by the availability of high-throughput technologies and a wide variety of bioinformatics tools. However, bioinformatics education and practice is still in its infancy in most of the African continent. Consequently, concerted efforts have been made in recent years to incorporate bioinformatics modules into biological sciences curriculum of African Universities. Despite this, one aspect of bioinformatics that is yet to be incorporated is structural bioinformatics. In this article, we report on a structural bioinformatics project carried out by final year project students in a Nigerian university. The target protein was the thermoacidophilic Sulfolobus islandicus rod-shaped virus 1 (SIRV1) Rep protein, which was further characterized using various free, user-friendly and online sequence-based and structure-based bioinformatics tools. This exercise gave students the opportunity to generate new data, interpret the data, and acquire collaborative research skills. In this report, emphasis is placed on analysis of the data generated to further encourage analytical skills. By sharing this experience, it is anticipated that other similar institutions would adopt parallel strategies to expose undergraduate students to structural biology, and increase awareness of freely available bioinformatics tools for tackling pertinent biological questions. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):547-554, 2018.
Collapse
Affiliation(s)
- Muse Oke
- Department of Biological Sciences, Fountain University, Oke-Osun, Osogbo, Nigeria
| | - Ramon Agbalajobi
- Department of Biological Sciences, Fountain University, Oke-Osun, Osogbo, Nigeria
| | | | - Babagana Muhammad
- Department of Biological Sciences, Fountain University, Oke-Osun, Osogbo, Nigeria
| | - Halimat Lawal
- Department of Biological Sciences, Fountain University, Oke-Osun, Osogbo, Nigeria
| | - Muhammad Mai
- Department of Biological Sciences, Fountain University, Oke-Osun, Osogbo, Nigeria
| | - Quadri Adegunle
- Department of Biological Sciences, Fountain University, Oke-Osun, Osogbo, Nigeria
| |
Collapse
|
19
|
|
20
|
Gaule TG, Smith MA, Tych KM, Pirrat P, Trinh CH, Pearson AR, Knowles PF, McPherson MJ. Oxygen Activation Switch in the Copper Amine Oxidase of Escherichia coli. Biochemistry 2018; 57:5301-5314. [PMID: 30110143 PMCID: PMC6136094 DOI: 10.1021/acs.biochem.8b00633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Copper amine oxidases (CuAOs) are metalloenzymes that reduce molecular oxygen to hydrogen peroxide during catalytic turnover of primary amines. In addition to Cu2+ in the active site, two peripheral calcium sites, ∼32 Å from the active site, have roles in Escherichia coli amine oxidase (ECAO). The buried Ca2+ (Asp533, Leu534, Asp535, Asp678, and Ala679) is essential for full-length protein production, while the surface Ca2+ (Glu573, Tyr667, Asp670, and Glu672) modulates biogenesis of the 2,4,5-trihydroxyphenylalanine quinone (TPQ) cofactor. The E573Q mutation at the surface site prevents calcium binding and TPQ biogenesis. However, TPQ biogenesis can be restored by a suppressor mutation (I342F) in the proposed oxygen delivery channel to the active site. While supporting TPQ biogenesis (∼60% WTECAO TPQ), I342F/E573Q has almost no amine oxidase activity (∼4.6% WTECAO activity). To understand how these long-range mutations have major effects on TPQ biogenesis and catalysis, we employed ultraviolet-visible spectroscopy, steady-state kinetics, inhibition assays, and X-ray crystallography. We show that the surface metal site controls the equilibrium (disproportionation) of the Cu2+-substrate reduced TPQ (TPQAMQ) Cu+-TPQ semiquinone (TPQSQ) couple. Removal of the calcium ion from this site by chelation or mutagenesis shifts the equilibrium to Cu2+-TPQAMQ or destabilizes Cu+-TPQSQ. Crystal structure analysis shows that TPQ biogenesis is stalled at deprotonation in the Cu2+-tyrosinate state. Our findings support WTECAO using the inner sphere electron transfer mechanism for oxygen reduction during catalysis, and while a Cu+-tyrosyl radical intermediate is not essential for TPQ biogenesis, it is required for efficient biogenesis.
Collapse
Affiliation(s)
- Thembaninkosi G Gaule
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences , University of Leeds , Leeds LS2 9JT , U.K
| | - Mark A Smith
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences , University of Leeds , Leeds LS2 9JT , U.K
| | - Katarzyna M Tych
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences , University of Leeds , Leeds LS2 9JT , U.K.,Physik-Department, Lehrstuhl für Biophysik E22 , Technische Universität München , D-85748 Garching , Germany
| | - Pascale Pirrat
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences , University of Leeds , Leeds LS2 9JT , U.K
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences , University of Leeds , Leeds LS2 9JT , U.K
| | - Arwen R Pearson
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences , University of Leeds , Leeds LS2 9JT , U.K.,Hamburg Centre of Ultrafast Imaging and Institute for Nanostructure and Solid State Physics , Universität Hamburg , D-22761 Hamburg , Germany
| | - Peter F Knowles
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences , University of Leeds , Leeds LS2 9JT , U.K
| | - Michael J McPherson
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences , University of Leeds , Leeds LS2 9JT , U.K
| |
Collapse
|
21
|
Mondal D, Majee MC, Kundu S, Mörtel M, Abbas G, Endo A, Khusniyarov MM, Chaudhury M. Dinuclear Iron(III) and Cobalt(III) Complexes Featuring a Biradical Bridge: Their Molecular Structures and Magnetic, Spectroscopic, and Redox Properties. Inorg Chem 2018; 57:1004-1016. [DOI: 10.1021/acs.inorgchem.7b02340] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dhrubajyoti Mondal
- Department of Inorganic
Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Mithun Chandra Majee
- Department of Inorganic
Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Sanchita Kundu
- Department of Inorganic
Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Max Mörtel
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Egerlandstrasse
1, 91058 Erlangen, Germany
| | - Ghulam Abbas
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Egerlandstrasse
1, 91058 Erlangen, Germany
| | - Akira Endo
- Department
of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1
Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan
| | - Marat M. Khusniyarov
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Egerlandstrasse
1, 91058 Erlangen, Germany
| | - Muktimoy Chaudhury
- Department of Inorganic
Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| |
Collapse
|
22
|
Muthuramalingam S, Subramaniyan S, Khamrang T, Velusamy M, Mayilmurugan R. Copper(II)-Bioinspired Models for Copper Amine Oxidases: Oxidative Half-Reaction in Water. ChemistrySelect 2017. [DOI: 10.1002/slct.201601786] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sethuraman Muthuramalingam
- Bioinorganic Chemistry Laboratory/Physical Chemistry; School of Chemistry; Madurai Kamaraj University; Madurai 625 021, Tamil Nadu India
| | - Shanmugam Subramaniyan
- Bioinorganic Chemistry Laboratory/Physical Chemistry; School of Chemistry; Madurai Kamaraj University; Madurai 625 021, Tamil Nadu India
| | - Themmila Khamrang
- Department of Chemistry; North Eastern Hill Universuty; Shillong- 793022 India
| | - Marappan Velusamy
- Department of Chemistry; North Eastern Hill Universuty; Shillong- 793022 India
| | - Ramasamy Mayilmurugan
- Bioinorganic Chemistry Laboratory/Physical Chemistry; School of Chemistry; Madurai Kamaraj University; Madurai 625 021, Tamil Nadu India
| |
Collapse
|
23
|
Bowen AM, Jones MW, Lovett JE, Gaule TG, McPherson MJ, Dilworth JR, Timmel CR, Harmer JR. Exploiting orientation-selective DEER: determining molecular structure in systems containing Cu(ii) centres. Phys Chem Chem Phys 2016; 18:5981-94. [DOI: 10.1039/c5cp06096f] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Analysis of orientation-selective DEER measurements using Cu(ii) centres in a series of molecules demonstrates its limits and capabilities in structure elucidation.
Collapse
Affiliation(s)
- Alice M. Bowen
- Centre for Advanced Electron Spin Resonance
- University of Oxford
- Oxford
- UK
- Institute of Physical and Theoretical Chemistry
| | - Michael W. Jones
- Centre for Advanced Electron Spin Resonance
- University of Oxford
- Oxford
- UK
| | - Janet E. Lovett
- Centre for Advanced Electron Spin Resonance
- University of Oxford
- Oxford
- UK
- SUPA
| | - Thembanikosi G. Gaule
- Astbury Centre for Structural Molecular Biology
- Institute of Molecular and Cellular Biology
- Faculty of Biological Sciences
- University of Leeds
- Leeds LS2 9JT
| | - Michael J. McPherson
- Astbury Centre for Structural Molecular Biology
- Institute of Molecular and Cellular Biology
- Faculty of Biological Sciences
- University of Leeds
- Leeds LS2 9JT
| | | | | | - Jeffrey R. Harmer
- Centre for Advanced Electron Spin Resonance
- University of Oxford
- Oxford
- UK
- Centre for Advanced Imaging
| |
Collapse
|
24
|
Hirano Y, Chonan K, Murayama K, Sakasegawa SI, Matsumoto H, Sugimori D. Syncephalastrum racemosum amine oxidase with high catalytic efficiency toward ethanolamine and its application in ethanolamine determination. Appl Microbiol Biotechnol 2015; 100:3999-4013. [PMID: 26691518 DOI: 10.1007/s00253-015-7198-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 11/17/2015] [Accepted: 11/24/2015] [Indexed: 10/22/2022]
Abstract
Our screening study yielded a copper amine oxidase (SrAOX) from Syncephalastrum racemosum, which showed much higher affinity and catalytic efficiency toward ethanolamine (EA) than any other amine oxidase (AOX). Following purification of the enzyme to electrophoretic homogeneity from a cell-free extract, the maximum activity toward EA was detected at pH 7.2-7.5 and 45 °C. The SrAOX complementary DNA (cDNA) was composed of a 2052-bp open reading frame encoding a 683-amino acid protein with a molecular mass of 77,162 Da. The enzyme functions as a homodimer. The deduced amino acid sequence of SrAOX showed 55.3 % identity to Rhizopus delemar AOX and contains two consensus sequences of Cu-AOX, NYDY, and HHQH, suggesting SrAOX is a type 1 Cu-AOX (i.e., a topaquinone enzyme). Structural homology modeling showed that residues (112)ML(113), (141)FADTWG(146) M158, and N318 are unique, and T144 possibly characterizes the substrate specificity of SrAOX. The recombinant enzyme (rSrAOX) was produced using Escherichia coli. Steady-state kinetic analysis of rSrAOX activity toward EA (pH 7.5 and 45 °C) gave K m and k cat values of 0.848 ± 0.009 mM and 9.11 ± 0.13 s(-1), respectively. The standard curves were linear between 0.1 and 2 mM EA, and 10 μg mL(-1)-2.5 mg mL(-1) (15 μM-3.6 mM) phosphatidylethanolamine using Streptomyces chromofuscus phospholipase D, respectively, was sufficiently sensitive for clinical use.
Collapse
Affiliation(s)
- Yoshitaka Hirano
- Department of Symbiotic Systems Science and Technology, Graduate School of Symbiotic Systems Science and Technology, Fukushima University, 1 Kanayagawa, Fukushima, 960-1296, Japan
| | - Keisuke Chonan
- Department of Symbiotic Systems Science and Technology, Graduate School of Symbiotic Systems Science and Technology, Fukushima University, 1 Kanayagawa, Fukushima, 960-1296, Japan
| | - Kazutaka Murayama
- Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University, 2-1 Seiryo, Aoba, Sendai, 980-8575, Japan
| | | | - Hideyuki Matsumoto
- Asahi Kasei Pharma Corp, 632-1 Mifuku, Izunokuni, Shizuoka, 410-2321, Japan
| | - Daisuke Sugimori
- Department of Symbiotic Systems Science and Technology, Graduate School of Symbiotic Systems Science and Technology, Fukushima University, 1 Kanayagawa, Fukushima, 960-1296, Japan.
| |
Collapse
|
25
|
Singh S, Singh AK, Wadhwa G, Singh DB, Dwivedi S, Gautam B, Ramteke PW. A Quantitative Measure of Conformational Changes in Apo, Holo and Ligand-Bound Forms of Enzymes. Interdiscip Sci 2015; 8:192-201. [PMID: 26260067 DOI: 10.1007/s12539-015-0284-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 11/10/2014] [Accepted: 11/26/2014] [Indexed: 10/23/2022]
Abstract
Determination of the native geometry of the enzymes and ligand complexes is a key step in the process of structure-based drug designing. Enzymes and ligands show flexibility in structural behavior as they come in contact with each other. When ligand binds with active site of the enzyme, in the presence of cofactor some structural changes are expected to occur in the active site. Motivation behind this study is to determine the nature of conformational changes as well as regions where such changes are more pronounced. To measure the structural changes due to cofactor and ligand complex, enzyme in apo, holo and ligand-bound forms is selected. Enzyme data set was retrieved from protein data bank. Fifteen triplet groups were selected for the analysis of structural changes based on selection criteria. Structural features for selected enzymes were compared at the global as well as local region. Accessible surface area for the enzymes in entire triplet set was calculated, which describes the change in accessible surface area upon binding of cofactor and ligand with the enzyme. It was observed that some structural changes take place during binding of ligand in the presence of cofactor. This study will helps in understanding the level of flexibility in protein-ligand interaction for computer-aided drug designing.
Collapse
Affiliation(s)
- Satendra Singh
- Department of Computational Biology and Bioinformatics, JSBB, SHIATS, Allahabad, 211007, India
| | - Atul Kumar Singh
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology, Mumbai, 400076, India
| | - Gulshan Wadhwa
- Apex Bioinformatics Centre, Department of Biotechnology, Ministry of Science and Technology, CGO Complex, Lodhi Road, New Delhi, 110003, India
| | - Dev Bukhsh Singh
- Department of Biotechnology, Institute of Biosciences and Biotechnology, Chhatrapati Shahu Ji Maharaj University, Kanpur, Uttar Pradesh, 208024, India.
| | - Seema Dwivedi
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, 201308, India
| | - Budhayash Gautam
- Department of Computational Biology and Bioinformatics, JSBB, SHIATS, Allahabad, 211007, India
| | - Pramod W Ramteke
- Department of Biological Sciences, SHIATS, Allahabad, 211007, India
| |
Collapse
|
26
|
Murakawa T, Hamaguchi A, Nakanishi S, Kataoka M, Nakai T, Kawano Y, Yamaguchi H, Hayashi H, Tanizawa K, Okajima T. Probing the Catalytic Mechanism of Copper Amine Oxidase from Arthrobacter globiformis with Halide Ions. J Biol Chem 2015; 290:23094-109. [PMID: 26269595 DOI: 10.1074/jbc.m115.662726] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Indexed: 11/06/2022] Open
Abstract
The catalytic reaction of copper amine oxidase proceeds through a ping-pong mechanism comprising two half-reactions. In the initial half-reaction, the substrate amine reduces the Tyr-derived cofactor, topa quinone (TPQ), to an aminoresorcinol form (TPQamr) that is in equilibrium with a semiquinone radical (TPQsq) via an intramolecular electron transfer to the active-site copper. We have analyzed this reductive half-reaction in crystals of the copper amine oxidase from Arthrobacter globiformis. Anerobic soaking of the crystals with an amine substrate shifted the equilibrium toward TPQsq in an "on-copper" conformation, in which the 4-OH group ligated axially to the copper center, which was probably reduced to Cu(I). When the crystals were soaked with substrate in the presence of halide ions, which act as uncompetitive and noncompetitive inhibitors with respect to the amine substrate and dioxygen, respectively, the equilibrium in the crystals shifted toward the "off-copper" conformation of TPQamr. The halide ion was bound to the axial position of the copper center, thereby preventing TPQamr from adopting the on-copper conformation. Furthermore, transient kinetic analyses in the presence of viscogen (glycerol) revealed that only the rate constant in the step of TPQamr/TPQsq interconversion is markedly affected by the viscogen, which probably perturbs the conformational change. These findings unequivocally demonstrate that TPQ undergoes large conformational changes during the reductive half-reaction.
Collapse
Affiliation(s)
- Takeshi Murakawa
- From the Department of Biochemistry, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Akio Hamaguchi
- the Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Shota Nakanishi
- the Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Misumi Kataoka
- the School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan, the Advanced Photon Technology Division, RIKEN SPring-8 Center, Sayo-gun, Hyogo 679-5148, Japan
| | - Tadashi Nakai
- the Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Yoshiaki Kawano
- the Advanced Photon Technology Division, RIKEN SPring-8 Center, Sayo-gun, Hyogo 679-5148, Japan
| | - Hiroshi Yamaguchi
- the School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan, the Advanced Photon Technology Division, RIKEN SPring-8 Center, Sayo-gun, Hyogo 679-5148, Japan
| | - Hideyuki Hayashi
- the Department of Chemistry, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan, and
| | - Katsuyuki Tanizawa
- the Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan, the Center of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, 783 71 Olomouc, Czech Republic
| | - Toshihide Okajima
- the Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan, the Department of Chemistry, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan, and
| |
Collapse
|
27
|
Shepard EM, Dooley DM. Inhibition and oxygen activation in copper amine oxidases. Acc Chem Res 2015; 48:1218-26. [PMID: 25897668 DOI: 10.1021/ar500460z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Copper-containing amine oxidases (CuAOs) use both copper and 2,4,5-trihydroxyphenylalanine quinone (TPQ) to catalyze the oxidative deamination of primary amines. The CuAO active site is highly conserved and comprised of TPQ and a mononuclear type II copper center that exhibits five-coordinate, distorted square pyramidal coordination geometry with histidine ligands and equatorially and axially bound water in the oxidized, resting state. The active site is buried within the protein, and CuAOs from various sources display remarkable diversity with respect to the composition of the active site channel and cofactor accessibility. Structural and mechanistic factors that influence substrate preference and inhibitor sensitivity and selectivity have been defined. This Account summarizes the strategies used to design selective CuAO inhibitors based on active site channel characteristics, leading to either enhanced steric fits or the trapping of reactive electrophilic products. These findings provide a framework to support the future development of candidate molecules aimed at minimizing the negative side effects associated with drugs containing amine functionalities. This is vital given the existence of human diamine oxidase and vascular adhesion protein-1, which have distinct amine substrate preferences and are associated with different metabolic processes. Inhibition of these enzymes by antifungal or antiprotozoal agents, as well as classic monoamine oxidase (MAO) inhibitors, may contribute to the adverse side effects associated with drug treatment. These observations provide a rationale for the limited clinical value associated with certain amine-containing pharmaceuticals and emphasize the need for more selective AO inhibitors. This Account also discusses the novel roles of copper and TPQ in the chemistry of O2 activation and substrate oxidation. Reduced CuAOs exist in a redox equilibrium between the Cu(II)-TPQAMQ (aminoquinol) and Cu(I)-TPQSQ (semiquinone). Elucidating the roles of Cu(I), TPQSQ, and TPQAMQ in O2 activation, for example, distinguishing inner-sphere versus outer-sphere electron transfer mechanisms, has been actively investigated since the discovery of TPQSQ in 1991 and has only recently been clarified. Kinetics and spectroscopic studies encompassing metal substitution, stopped-flow and temperature-jump relaxation methods, and oxygen kinetic isotope experiments have provided strong support for an inner-sphere electron transfer step from Cu(I) to O2. Data for two enzymes support a mechanism wherein O2 prebinds to a three-coordinate Cu(I) site, yielding a [Cu(II)(η(1)-O2(-1))](+) intermediate, with H2O2 generated from ensuing rate-determining proton coupled electron transfer from TPQSQ. While kinetics data from the cobalt-substituted yeast enzyme indicated that O2 is reduced through an outer-sphere process involving TPQAMQ, new findings with a bacterial CuAO demonstrate that both the Cu(II) and Co(II) forms of the enzyme operate via parallel mechanisms involving metal-superoxide intermediates. Structural observations of a coordinated TPQSQ-Cu(I) complex in two CuAOs supports previous indications that Cu(II)/(I) ligand substitution chemistry may be mechanistically relevant. Substantial evidence indicates that rapid and reversible inner-sphere reduction of O2 at a three-coordinate Cu(I) site occurs, but the existence of a coordinated semiquinone in some AOs suggests that, in these enzymes, an outer-sphere reaction between O2 and TPQSQ may also be possible, since this is expected to be energetically favorable compared with outer-sphere electron transfer from TPQAMQ to O2.
Collapse
Affiliation(s)
- Eric M. Shepard
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - David M. Dooley
- Office
of the President, University of Rhode Island, Kingston, Rhode Island 02881, United States
| |
Collapse
|
28
|
Holder PG, Jones LC, Drake PM, Barfield RM, Bañas S, de Hart GW, Baker J, Rabuka D. Reconstitution of Formylglycine-generating Enzyme with Copper(II) for Aldehyde Tag Conversion. J Biol Chem 2015; 290:15730-15745. [PMID: 25931126 PMCID: PMC4505483 DOI: 10.1074/jbc.m115.652669] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Indexed: 01/01/2023] Open
Abstract
To further our aim of synthesizing aldehyde-tagged proteins for research and biotechnology applications, we developed methods for recombinant production of aerobic formylglycine-generating enzyme (FGE) in good yield. We then optimized the FGE biocatalytic reaction conditions for conversion of cysteine to formylglycine in aldehyde tags on intact monoclonal antibodies. During the development of these conditions, we discovered that pretreating FGE with copper(II) is required for high turnover rates and yields. After further investigation, we confirmed that both aerobic prokaryotic (Streptomyces coelicolor) and eukaryotic (Homo sapiens) FGEs contain a copper cofactor. The complete kinetic parameters for both forms of FGE are described, along with a proposed mechanism for FGE catalysis that accounts for the copper-dependent activity.
Collapse
Affiliation(s)
| | - Lesley C Jones
- From Catalent Pharma Solutions, Emeryville, California 94608
| | | | | | - Stefanie Bañas
- From Catalent Pharma Solutions, Emeryville, California 94608
| | | | - Jeanne Baker
- From Catalent Pharma Solutions, Emeryville, California 94608
| | - David Rabuka
- From Catalent Pharma Solutions, Emeryville, California 94608.
| |
Collapse
|
29
|
Singh S, Singh AK, Wadhwa G, Singh DB, Dwivedi S, Gautam B, Ramteke PW. A quantitative measure of conformational changes in Apo, holo and ligand bound form of enzymes. Interdiscip Sci 2015. [PMID: 25863964 DOI: 10.1007/s12539-014-0251-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 11/10/2014] [Accepted: 11/26/2014] [Indexed: 06/04/2023]
Abstract
Determination of the native geometry of the enzymes and ligand complexe is a key step in the process of structure based drug designing. Enzymes and ligands show flexibility in structural behavior as they come in contact with each other. When ligand binds with active site of the enzyme, in presence of cofactor some structural changes are expected to occur in the active site. Motivation behind this study is to determine the nature of conformational changes as well as regions where such changes are more pronounced. To measure the structural changes due to cofactor and ligand complex, enzyme in Apo, holo and ligand bound form is selected. Enzyme data set was retrieved from protein data bank (PDB). 15 triplet groups were selected for the analysis of structural changes based on selection criteria. Structural features for selected enzymes were compared at the global as well as local region. Accessible surface area for the enzymes in entire triplet set was calculated, which describes the change in accessible surface area upon binding of cofactor and ligand with the enzyme. It was observed that some structural changes take place during binding of ligand in presence of cofactor. This study will helps in understanding the level of flexibility in protein-ligand interaction for computer aided drug designing.
Collapse
Affiliation(s)
- Satendra Singh
- Department of Computational Biology & Bioinformatics, JSBB, SHIATS, Allahabad, 211007, India
| | | | | | | | | | | | | |
Collapse
|
30
|
Chacón-Verdú MD, Campillo-Brocal JC, Lucas-Elío P, Davidson VL, Sánchez-Amat A. Characterization of recombinant biosynthetic precursors of the cysteine tryptophylquinone cofactors of l-lysine-epsilon-oxidase and glycine oxidase from Marinomonas mediterranea. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:1123-31. [PMID: 25542375 DOI: 10.1016/j.bbapap.2014.12.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/12/2014] [Accepted: 12/15/2014] [Indexed: 01/31/2023]
Abstract
The lysine-ε-oxidase, LodA, and glycine oxidase, GoxA, from Marinomonas mediteranea each possesses a cysteine tryptophylquinone (CTQ) cofactor. This cofactor is derived from posttranslational modifications which are covalent crosslinking of tryptophan and cysteine residues and incorporation of two oxygen atoms into the indole ring of Trp. In this manuscript, it is shown that the recombinant synthesis of LodA and GoxA containing a fully synthesized CTQ cofactor requires coexpression of a partner flavoprotein, LodB for LodA and GoxB for GoxA, which are not interchangeable. An inactive precursor of LodA or GoxA which contained a monohydroxylated Trp residue and no crosslink to the Cys was isolated from the soluble fraction when they were expressed alone. The structure of LodA revealed an Asp residue close to the cofactor which is conserved in quinohemoprotein amine dehydrogenase (QHNDH), containing CTQ, and methylamine dehydrogenase (MADH) containing tryptophan tryptophylquinone (TTQ) as cofactor. To study the role of this residue in the synthesis of the LodA precursor, Asp-512 was mutated to Ala. When the mutant protein was coexpressed with LodB an inactive protein was isolated which was soluble and contained no modifications at all, suggesting a role for this Asp in the initial LodB-independent hydroxylation of Trp. A similar role had been proposed for this conserved Asp residue in MADH. It is noteworthy that the formation of TTQ in MADH from the precursor also requires an accessory enzyme for its biosynthesis but it is a diheme enzyme MauG and not a flavoprotein. The results presented reveal novel mechanisms of post-translational modification involved in the generation of protein-derived cofactors. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.
Collapse
Affiliation(s)
- María Dolores Chacón-Verdú
- Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia 30100, Spain.
| | - Jonatan C Campillo-Brocal
- Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia 30100, Spain.
| | - Patricia Lucas-Elío
- Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia 30100, Spain.
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA.
| | - Antonio Sánchez-Amat
- Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia 30100, Spain.
| |
Collapse
|
31
|
Solomon EI, Heppner DE, Johnston EM, Ginsbach JW, Cirera J, Qayyum M, Kieber-Emmons MT, Kjaergaard CH, Hadt RG, Tian L. Copper active sites in biology. Chem Rev 2014; 114:3659-853. [PMID: 24588098 PMCID: PMC4040215 DOI: 10.1021/cr400327t] [Citation(s) in RCA: 1138] [Impact Index Per Article: 113.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - David E. Heppner
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | - Jake W. Ginsbach
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Jordi Cirera
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Munzarin Qayyum
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | | | - Ryan G. Hadt
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Li Tian
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| |
Collapse
|
32
|
Finney J, Moon HJ, Ronnebaum T, Lantz M, Mure M. Human copper-dependent amine oxidases. Arch Biochem Biophys 2014; 546:19-32. [PMID: 24407025 DOI: 10.1016/j.abb.2013.12.022] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/24/2013] [Accepted: 12/26/2013] [Indexed: 12/11/2022]
Abstract
Copper amine oxidases (CAOs) are a class of enzymes that contain Cu(2+) and a tyrosine-derived quinone cofactor, catalyze the conversion of a primary amine functional group to an aldehyde, and generate hydrogen peroxide and ammonia as byproducts. These enzymes can be classified into two non-homologous families: 2,4,5-trihydroxyphenylalanine quinone (TPQ)-dependent CAOs and the lysine tyrosylquinone (LTQ)-dependent lysyl oxidase (LOX) family of proteins. In this review, we will focus on recent developments in the field of research concerning human CAOs and the LOX family of proteins. The aberrant expression of these enzymes is linked to inflammation, fibrosis, tumor metastasis/invasion and other diseases. Consequently, there is a critical need to understand the functions of these proteins at the molecular level, so that strategies targeting these enzymes can be developed to combat human diseases.
Collapse
Affiliation(s)
- Joel Finney
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
| | - Hee-Jung Moon
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
| | - Trey Ronnebaum
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
| | - Mason Lantz
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
| | - Minae Mure
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
| |
Collapse
|
33
|
Murakawa T, Hayashi H, Sunami T, Kurihara K, Tamada T, Kuroki R, Suzuki M, Tanizawa K, Okajima T. High-resolution crystal structure of copper amine oxidase fromArthrobacter globiformis: assignment of bound diatomic molecules as O2. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2483-94. [DOI: 10.1107/s0907444913023196] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 08/18/2013] [Indexed: 11/10/2022]
Abstract
The crystal structure of a copper amine oxidase fromArthrobacter globiformiswas determined at 1.08 Å resolution with the use of low-molecular-weight polyethylene glycol (LMW PEG; average molecular weight ∼200) as a cryoprotectant. The final crystallographicRfactor andRfreewere 13.0 and 15.0%, respectively. Several molecules of LMW PEG were found to occupy cavities in the protein interior, including the active site, which resulted in a marked reduction in the overallBfactor and consequently led to a subatomic resolution structure for a relatively large protein with a monomer molecular weight of ∼70 000. About 40% of the presumed H atoms were observed as clear electron densities in theFo−Fcdifference map. Multiple minor conformers were also identified for many residues. Anisotropic displacement fluctuations were evaluated in the active site, which contains a post-translationally derived quinone cofactor and a Cu atom. Furthermore, diatomic molecules, most likely to be molecular oxygen, are bound to the protein, one of which is located in a region that had previously been proposed as an entry route for the dioxygen substrate from the central cavity of the dimer interface to the active site.
Collapse
|
34
|
Johnson BJ, Yukl ET, Klema VJ, Klinman JP, Wilmot CM. Structural snapshots from the oxidative half-reaction of a copper amine oxidase: implications for O2 activation. J Biol Chem 2013; 288:28409-17. [PMID: 23940035 DOI: 10.1074/jbc.m113.501791] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mechanism of molecular oxygen activation is the subject of controversy in the copper amine oxidase family. At their active sites, copper amine oxidases contain both a mononuclear copper ion and a protein-derived quinone cofactor. Proposals have been made for the activation of molecular oxygen via both a Cu(II)-aminoquinol catalytic intermediate and a Cu(I)-semiquinone intermediate. Using protein crystallographic freeze-trapping methods under low oxygen conditions combined with single-crystal microspectrophotometry, we have determined structures corresponding to the iminoquinone and semiquinone forms of the enzyme. Methylamine reduction at acidic or neutral pH has revealed protonated and deprotonated forms of the iminoquinone that are accompanied by a bound oxygen species that is likely hydrogen peroxide. However, methylamine reduction at pH 8.5 has revealed a copper-ligated cofactor proposed to be the semiquinone form. A copper-ligated orientation, be it the sole identity of the semiquinone or not, blocks the oxygen-binding site, suggesting that accessibility of Cu(I) may be the basis of partitioning O2 activation between the aminoquinol and Cu(I).
Collapse
Affiliation(s)
- Bryan J Johnson
- From the Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455 and
| | | | | | | | | |
Collapse
|
35
|
Liu Y, Mukherjee A, Nahumi N, Ozbil M, Brown D, Angeles-Boza AM, Dooley DM, Prabhakar R, Roth JP. Experimental and Computational Evidence of Metal-O2 Activation and Rate-Limiting Proton-Coupled Electron Transfer in a Copper Amine Oxidase. J Phys Chem B 2012; 117:218-29. [DOI: 10.1021/jp3121484] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yi Liu
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - Arnab Mukherjee
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - Nadav Nahumi
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - Mehmet Ozbil
- Department of Chemistry, University of Miami, 1301 Memorial Drive,
Coral Gables, Florida 33146, United States
| | - Doreen Brown
- Department of Chemistry
and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Alfredo M. Angeles-Boza
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - David M. Dooley
- Department of Chemistry
and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive,
Coral Gables, Florida 33146, United States
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| |
Collapse
|
36
|
Lovett JE, Lovett BW, Harmer J. DEER-Stitch: combining three- and four-pulse DEER measurements for high sensitivity, deadtime free data. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 223:98-106. [PMID: 22975240 DOI: 10.1016/j.jmr.2012.08.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 07/20/2012] [Accepted: 08/13/2012] [Indexed: 06/01/2023]
Abstract
Over approximately the last 15 years the electron paramagnetic resonance (EPR) technique of double electron electron resonance (DEER) has attracted considerable attention since it allows for the precise measurement of the dipole-dipole coupling between radicals and thus can lead to distance information between pairs of radicals separated by up to ca. 8 nm. The "deadtime free" 4-pulse DEER sequence is widely used but can suffer from poor sensitivity if the electron spin-echo decays too quickly to allow collection of a sufficiently long time trace. In this paper we present a method which takes advantage of the much greater sensitivity that the 3-pulse sequence offers over the 4-pulse sequence since the measured electron spin-echo intensity (for equal sequence lengths) is greater. By combining 3- and 4-pulse DEER time traces using a method coined DEER-Stitch (DEERS) accurate dipole-dipole coupling measurements can be made which combine the sensitivity of the 3-pulse DEER sequence with the deadtime free advantage of the 4-pulse DEER sequence. To develop the DEER-Stitch method three systems were measured: a semi-rigid bis-nitroxide labeled nanowire, the bis-nitroxide labeled protein CD55 with a distance between labels of almost 8 nm and a dimeric copper amine oxidase from Arthrobacter globiformis (AGAO).
Collapse
Affiliation(s)
- J E Lovett
- EaStCHEM School of Chemistry, Joseph Black Building, The King's Buildings, Edinburgh EH9 3JJ, UK.
| | | | | |
Collapse
|
37
|
Klema VJ, Johnson BJ, Klinman JP, Wilmot CM. The precursor form of Hansenula polymorpha copper amine oxidase 1 in complex with CuI and CoII. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:501-10. [PMID: 22691777 PMCID: PMC3374502 DOI: 10.1107/s1744309112012857] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 03/23/2012] [Indexed: 11/10/2022]
Abstract
Copper amine oxidases (CAOs) catalyze the oxidative deamination of primary amines to their corresponding aldehydes, with the concomitant reduction of O(2) to H(2)O(2). Catalysis requires two cofactors: a mononuclear copper center and the cofactor 2,4,5-trihydroxyphenylalanine quinone (TPQ). TPQ is synthesized through the post-translational modification of an endogenous tyrosine residue and requires only oxygen and copper to proceed. TPQ biogenesis in CAO can be supported by alternate metals, albeit at decreased rates. A variety of factors are thought to contribute to the degree to which a metal can support TPQ biogenesis, including Lewis acidity, redox potential and electrostatic stabilization capability. The crystal structure has been solved of one of two characterized CAOs from the yeast Hansenula polymorpha (HPAO-1) in its metal-free (apo) form, which contains an unmodified precursor tyrosine residue instead of fully processed TPQ (HPAO-1 was denoted HPAO in the literature prior to 2010). Structures of apoHPAO-1 in complex with Cu(I) and Co(II) have also been solved, providing structural insight into metal binding prior to biogenesis.
Collapse
Affiliation(s)
- Valerie J. Klema
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN 55455, USA
| | - Bryan J. Johnson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN 55455, USA
| | - Judith P. Klinman
- Department of Chemistry and Department of Molecular and Cell Biology, and the California Institute of Quantitative Biosciences (QB3), University of California, 608C Stanley Hall, Berkeley, CA 94720, USA
| | - Carrie M. Wilmot
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN 55455, USA
| |
Collapse
|
38
|
Mills SA, Brown DE, Dang K, Sommer D, Bitsimis A, Nguyen J, Dooley DM. Cobalt substitution supports an inner-sphere electron transfer mechanism for oxygen reduction in pea seedling amine oxidase. J Biol Inorg Chem 2012; 17:507-15. [PMID: 22258083 DOI: 10.1007/s00775-011-0872-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Accepted: 12/29/2011] [Indexed: 10/14/2022]
Abstract
Copper amine oxidases (CAOs) are a large family of proteins that use molecular oxygen to oxidize amines to aldehydes with the concomitant production of hydrogen peroxide and ammonia. CAOs utilize two cofactors for this reaction: topaquinone (TPQ) and a Cu(II) ion. Two mechanisms for oxygen reduction have been proposed for these enzymes. In one mechanism (involving inner-sphere electron transfer to O(2)), Cu(II) is reduced by TPQ, forming Cu(I), to which O(2) binds, forming a copper-superoxide complex. In an alternative mechanism (involving outer-sphere electron transfer to O(2)), O(2) is directly reduced by TPQ, without reduction of Cu(II). Substitution of Cu(II) with Co(II) has been used to distinguish between the two mechanisms in several CAOs. Because it is unlikely that Co(II) could be reduced to Co(I) in this environment, an inner-sphere mechanism, as described above, is prevented. We adapted metal replacement methods used for other CAOs to the amine oxidase from pea seedlings (PSAO). Cobalt-substituted PSAO (CoPSAO) displayed nominal catalytic activity: k(cat) is 4.7% of the native k(cat), and K(M) (O(2)) for CoPSAO is substantially (22-fold) higher. The greatly reduced turnover number for CoPSAO suggests that PSAO uses the inner-sphere mechanism, as has been predicted from (18)O isotope effect studies (Mukherjee et al. in J Am Chem Soc 130:9459-9473, 2008), and is catalytically compromised when constrained to operate via outer-sphere electron transfer to O(2). This study, together with previous work, provides strong evidence that CAOs use both proposed mechanisms, but each homolog may prefer one mechanism over the other.
Collapse
Affiliation(s)
- Stephen A Mills
- Department of Chemistry and Biochemistry, University of San Diego, 5998 Alcala Park, San Diego, CA 92110, USA.
| | | | | | | | | | | | | |
Collapse
|
39
|
Yuan H, Xin Y, Hamelberg D, Gadda G. Insights on the Mechanism of Amine Oxidation Catalyzed by d-Arginine Dehydrogenase Through pH and Kinetic Isotope Effects. J Am Chem Soc 2011; 133:18957-65. [DOI: 10.1021/ja2082729] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hongling Yuan
- Department of Chemistry, ‡Department of Biology, and §The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
| | - Yao Xin
- Department of Chemistry, ‡Department of Biology, and §The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
| | - Donald Hamelberg
- Department of Chemistry, ‡Department of Biology, and §The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
| | - Giovanni Gadda
- Department of Chemistry, ‡Department of Biology, and §The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
| |
Collapse
|
40
|
Murakawa T, Hayashi H, Taki M, Yamamoto Y, Kawano Y, Tanizawa K, Okajima T. Structural insights into the substrate specificity of bacterial copper amine oxidase obtained by using irreversible inhibitors. J Biochem 2011; 151:167-78. [PMID: 21984603 DOI: 10.1093/jb/mvr125] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Copper amine oxidases (CAOs) catalyse the oxidation of various aliphatic amines to the corresponding aldehydes, ammonia and hydrogen peroxide. Although CAOs from various organisms share a highly conserved active-site structure including a protein-derived cofactor, topa quinone (TPQ), their substrate specificities differ considerably. To obtain structural insights into the substrate specificity of a CAO from Arthrobacter globiformis (AGAO), we have determined the X-ray crystal structures of AGAO complexed with irreversible inhibitors that form covalent adducts with TPQ. Three hydrazine derivatives, benzylhydrazine (BHZ), 4-hydroxybenzylhydrazine (4-OH-BHZ) and phenylhydrazine (PHZ) formed predominantly a hydrazone adduct, which is structurally analogous to the substrate Schiff base of TPQ formed during the catalytic reaction. With BHZ and 4-OH-BHZ, but not with PHZ, the inhibitor aromatic ring is bound to a hydrophobic cavity near the active site in a well-defined conformation. Furthermore, the hydrogen atom on the hydrazone nitrogen is located closer to the catalytic base in the BHZ and 4-OH-BHZ adducts than in the PHZ adduct. These results correlate well with the reactivity of 2-phenylethylamine and tyramine as preferred substrates for AGAO and also explain why benzylamine is a poor substrate with markedly decreased rate constants for the steps of proton abstraction and the following hydrolysis.
Collapse
Affiliation(s)
- Takeshi Murakawa
- Department of Biochemistry, Osaka Medical College, Osaka 569-8686, Japan
| | | | | | | | | | | | | |
Collapse
|
41
|
Largeron M. Amine oxidases of the quinoproteins family: Their implication in the metabolic oxidation of xenobiotics. ANNALES PHARMACEUTIQUES FRANÇAISES 2011; 69:53-61. [DOI: 10.1016/j.pharma.2010.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 10/04/2010] [Accepted: 10/13/2010] [Indexed: 12/11/2022]
|
42
|
Smith MA, Pirrat P, Pearson AR, Kurtis CRP, Trinh CH, Gaule TG, Knowles PF, Phillips SEV, McPherson MJ. Exploring the roles of the metal ions in Escherichia coli copper amine oxidase. Biochemistry 2010; 49:1268-80. [PMID: 20052994 PMCID: PMC2817917 DOI: 10.1021/bi901738k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To investigate the role of the active site copper in Escherichia coli copper amine oxidase (ECAO), we initiated a metal-substitution study. Copper reconstitution of ECAO (Cu-ECAO) restored only approximately 12% wild-type activity as measured by k(cat(amine)). Treatment with EDTA, to remove exogenous divalent metals, increased Cu-ECAO activity but reduced the activity of wild-type ECAO. Subsequent addition of calcium restored wild-type ECAO and further enhanced Cu-ECAO activities. Cobalt-reconstituted ECAO (Co-ECAO) showed lower but significant activity. These initial results are consistent with a direct electron transfer from TPQ to oxygen stabilized by the metal. If a Cu(I)-TPQ semiquinone mechanism operates, then an alternative outer-sphere electron transfer must also exist to account for the catalytic activity of Co-ECAO. The positive effect of calcium on ECAO activity led us to investigate the peripheral calcium binding sites of ECAO. Crystallographic analysis of wild-type ECAO structures, determined in the presence and absence of EDTA, confirmed that calcium is the normal ligand of these peripheral sites. The more solvent exposed calcium can be easily displaced by mono- and divalent cations with no effect on activity, whereas removal of the more buried calcium ion with EDTA resulted in a 60-90% reduction in ECAO activity and the presence of a lag phase, which could be overcome under oxygen saturation or by reoccupying the buried site with various divalent cations. Our studies indicate that binding of metal ions in the peripheral sites, while not essential, is important for maximal enzymatic activity in the mature enzyme.
Collapse
Affiliation(s)
- Mark A Smith
- Astbury Centre for Structural Molecular Biology and Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Das A, Sarkar B, Duboc C, Strobel S, Fiedler J, Záliš S, Lahiri G, Kaim W. Das ungeradzahlig elektronenkonfigurierte Komplexion [Ruk(NOm)(Qn)(terpy)]2+mit zwei idealtypischen “nicht-unschuldigen” Liganden. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900767] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
44
|
Das A, Sarkar B, Duboc C, Strobel S, Fiedler J, Záliš S, Lahiri G, Kaim W. An Odd-Electron Complex [Ruk(NOm)(Qn)(terpy)]2+with Two Prototypical Non-Innocent Ligands. Angew Chem Int Ed Engl 2009; 48:4242-5. [DOI: 10.1002/anie.200900767] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
45
|
Arima J, Uesugi Y, Hatanaka T. Bacillus d-stereospecific metallo-amidohydrolase: Active-site metal-ion substitution changes substrate specificity. Biochimie 2009; 91:568-76. [DOI: 10.1016/j.biochi.2009.01.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
46
|
Shepard EM, Okonski KM, Dooley DM. Kinetics and spectroscopic evidence that the Cu(I)-semiquinone intermediate reduces molecular oxygen in the oxidative half-reaction of Arthrobacter globiformis amine oxidase. Biochemistry 2009; 47:13907-20. [PMID: 19053231 DOI: 10.1021/bi8011516] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The role of copper during the reoxidation of substrate-reduced amine oxidases by O(2) has not yet been definitively established. Both outer-sphere and inner-sphere pathways for the reduction of O(2) to H(2)O(2) have been proposed. A key step in the inner-sphere mechanism is the reaction of O(2) directly with the Cu(I) center of a Cu(I)-semiquinone intermediate. To thoroughly examine this possibility, we have measured the spectral changes associated with single-turnover reoxidation by O(2) of substrate-reduced Arthrobacter globiformis amine oxidase (AGAO) under a wide range of conditions. We have previously demonstrated that the internal electron-transfer reaction [Cu(II)-TPQ(AMQ) --> Cu(I)-TPQ(SQ)] (where TPQ(AMQ) is the aminoquinol form of reduced TPQ and TPQ(SQ) is the semiquinone form) occurs at a rate that could permit the reaction of O(2) with both species to be observed on the stopped-flow time scale [Shepard, E. M., and Dooley, D. M. (2006) J. Biol. Inorg. Chem. 11, 1039-1048]. The transient absorption spectra observed for the reaction of O(2) with substrate-reduced AGAO provide compelling support for the reaction of the Cu(I)-TPQ(SQ) form. Further, global analysis of the kinetics and the transient absorption spectra are fully consistent with an inner-sphere reaction of the Cu(I)-semiquinone intermediate with O(2) and are inconsistent with an outer-sphere mechanism for the reaction of the reduced enzyme with O(2).
Collapse
Affiliation(s)
- Eric M Shepard
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
| | | | | |
Collapse
|
47
|
Taki M, Murakawa T, Nakamoto T, Uchida M, Hayashi H, Tanizawa K, Yamamoto Y, Okajima T. Further insight into the mechanism of stereoselective proton abstraction by bacterial copper amine oxidase. Biochemistry 2008; 47:7726-33. [PMID: 18627131 DOI: 10.1021/bi800623f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
During the catalytic reaction of copper amine oxidase, one of the two prochiral hydrogen atoms at the C1 position of substrate amine is stereoselectively abstracted by a conserved Asp residue serving as a general base. Using stereospecifically deuterium-labeled enantiomers of 2-phenylethylamine, we previously showed that the pro-S alpha-proton is abstracted by the enzyme from Arthrobacter globiformis (AGAO) [Uchida, M., et al. (2003) Biosci. Biotechnol. Biochem. 67, 2664-2667]. More recently, we have also demonstrated that the pro-S selectivity of alpha-proton abstraction is fully retained even in the reaction of a mutant AGAO lacking the catalytic base [Chiu, Y.-C., et al. (2006) Biochemistry 45, 4105-4120]. On the basis of these findings, we have proposed that the stereoselectivity of alpha-proton abstraction is primarily determined by the conformation of the Schiff base intermediate formed between the substrate and the topa quinone cofactor (TPQ), stabilized by the binding of the distal part of the substrate to a hydrophobic pocket of the enzyme. In this conformation, the pro-S hydrogen atom to be abstracted is nearly perpendicular to the plane of the Schiff base-TPQ conjugate system, achieving the maximum overlap of sigma- and pi-orbitals. To further elucidate the stereochemical details, we have synthesized stereospecifically deuterium-labeled enantiomers of ethylamine, a very poor substrate for AGAO, in addition to those structurally related to the preferred substrate, 2-phenylethylamine. In marked contrast to the nearly complete pro-S selectivity of alpha-proton abstraction for most substrates that have been examined, the stereoselectivity for ethylamine decreased significantly to as little as 88%. The crystal structure of AGAO soaked with ethylamine showed very poor electron densities for the substrate Schiff base intermediate, showing that its conformation is not defined uniquely. Thus, the stereoselectivity of alpha-proton abstraction during the copper amine oxidase reaction is closely associated with the conformational flexibility of the substrate Schiff base intermediate.
Collapse
Affiliation(s)
- Masayasu Taki
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Langley DB, Trambaiolo DM, Duff AP, Dooley DM, Freeman HC, Guss JM. Complexes of the copper-containing amine oxidase from Arthrobacter globiformis with the inhibitors benzylhydrazine and tranylcypromine. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:577-83. [PMID: 18607080 PMCID: PMC2443983 DOI: 10.1107/s174430910801556x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Accepted: 05/23/2008] [Indexed: 11/10/2022]
Abstract
Complexes of Arthrobacter globiformis amine oxidase (AGAO) with the inhibitors benzylhydrazine and tranylcypromine (an antidepressant drug) have been refined at 1.86 and 1.65 A resolution, respectively. Both inhibitors form covalent adducts with the TPQ cofactor. A tyrosine residue, proposed to act as a gate to the AGAO active site, is in its open conformation.
Collapse
Affiliation(s)
- David B Langley
- School of Molecular and Microbial Biosciences, University of Sydney, Australia
| | | | | | | | | | | |
Collapse
|
49
|
Carter SM, Sia A, Shaw MJ, Heyduk AF. Isolation and characterization of a neutral imino-semiquinone radical. J Am Chem Soc 2008; 130:5838-9. [PMID: 18402446 DOI: 10.1021/ja711185s] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The neutral imino-semiquinone, 4,6-di-tert-butyl-2-tert-butylimino-semiquinone (isqH.), can be prepared by a conproportionation of the parent aminophenol and iminoquinone compounds. The neutral radical species has been characterized in the solid state by X-ray diffraction and in solution by EPR and UV-vis absorption spectroscopy. The stability of the open-shell radical is derived from the basicity of the tert-butylimino group and the intramolecular hydrogen bond.
Collapse
Affiliation(s)
- Shawn M Carter
- Department of Chemistry, University of California, Irvine, California, 92697, USA
| | | | | | | |
Collapse
|
50
|
Welford RWD, Lam A, Mirica LM, Klinman JP. Partial conversion of Hansenula polymorpha amine oxidase into a "plant" amine oxidase: implications for copper chemistry and mechanism. Biochemistry 2007; 46:10817-27. [PMID: 17760423 DOI: 10.1021/bi700943r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of the first electron transfer from reduced cofactor to O2 in the catalytic cycle of copper amine oxidases (CAOs) remains controversial. Two possibilities have been proposed. In the first mechanism, the reduced aminoquinol form of the TPQ cofactor transfers an electron to the copper, giving radical semiquinone and Cu(I), the latter of which reduces O2 (pathway 1). The second mechanism invokes direct transfer of the first electron from the reduced aminoquinol form of the TPQ cofactor to O2 (pathway 2). The debate over these mechanisms has arisen, in part, due to variable experimental observations with copper amine oxidases from plant versus other eukaryotic sources. One important difference is the position of the aminoquinol/Cu(II) to semiquinone/Cu(I) equilibrium on anaerobic reduction with amine substrate, which varies from almost 0% to 40% semiquinone/Cu(I). In this study we have shown how protein structure controls this equilibrium by making a single-point mutation at a second-sphere ligand to the copper, D630N in Hansenula polymorpha amine oxidase, which greatly increases the concentration of the cofactor semiquinone/Cu(I) following anaerobic reduction by substrate. The catalytic properties of this mutant, including 18O kinetic isotope effects, point to a conservation of pathway 2, despite the elevated production of the cofactor semiqunone/Cu(I). Changes in kcat/Km[O2] are attributed to an impact of D630N on an increased affinity of O2 for its hydrophobic pocket. The data in this study indicate that changes in cofactor semiquinone/Cu(I) levels are not sufficient to alter the mechanism of O2 reduction and illuminate how subtle features are able to control the reduction potential of active site metals in proteins.
Collapse
Affiliation(s)
- Richard W D Welford
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
| | | | | | | |
Collapse
|