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Danaf NA, Kretzschmar J, Jahn B, Singer H, Pol A, Op den Camp HJM, Steudtner R, Lamb DC, Drobot B, Daumann LJ. Studies of pyrroloquinoline quinone species in solution and in lanthanide-dependent methanol dehydrogenases. Phys Chem Chem Phys 2022; 24:15397-15405. [PMID: 35704886 DOI: 10.1039/d2cp00311b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pyrroloquinoline quinone (PQQ) is a redox cofactor in calcium- and lanthanide-dependent alcohol dehydrogenases that has been known and studied for over 40 years. Despite its long history, many questions regarding its fluorescence properties, speciation in solution and in the active site of alcohol dehydrogenase remain open. Here we investigate the effects of pH and temperature on the distribution of different PQQ species (H3PQQ to PQQ3- in addition to water adducts and in complex with lanthanides) with NMR and UV-Vis spectroscopy as well as time-resolved laser-induced fluorescence spectroscopy (TRLFS). Using a europium derivative from a new, recently-discovered class of lanthanide-dependent methanol dehydrogenase (MDH) enzymes, we utilized two techniques to monitor Ln binding to the active sites of these enzymes. Employing TRLFS, we were able to follow Eu(III) binding directly to the active site of MDH using its luminescence and could quantify three Eu(III) states: Eu(III) in the active site of MDH, but also in solution as PQQ-bound Eu(III) and in the aquo-ion form. Additionally, we used the antenna effect to study PQQ and simultaneously Eu(III) in the active site.
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Affiliation(s)
- Nader Al Danaf
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5 - 13, 81377 München, Germany. .,Center for NanoScience, Ludwig-Maximilians-University Munich, Geschwister-Scholl Platz 1, 80539 München, Germany
| | - Jerome Kretzschmar
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf e.V., Bautzner Landstraße 400, 01328 Dresden, Germany.
| | - Berenice Jahn
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5 - 13, 81377 München, Germany.
| | - Helena Singer
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5 - 13, 81377 München, Germany.
| | - Arjan Pol
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Robin Steudtner
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf e.V., Bautzner Landstraße 400, 01328 Dresden, Germany.
| | - Don C Lamb
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5 - 13, 81377 München, Germany. .,Center for NanoScience, Ludwig-Maximilians-University Munich, Geschwister-Scholl Platz 1, 80539 München, Germany
| | - Björn Drobot
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf e.V., Bautzner Landstraße 400, 01328 Dresden, Germany.
| | - Lena J Daumann
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5 - 13, 81377 München, Germany.
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2
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Schäfer A, Vetsova VA, Schneider EK, Kappes M, Seitz M, Daumann LJ, Weis P. Ion Mobility Studies of Pyrroloquinoline Quinone Aza-Crown Ether-Lanthanide Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:722-730. [PMID: 35300493 DOI: 10.1021/jasms.2c00023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Lanthanide-dependent enzymes and their biomimetic complexes have arisen as an interesting target of research in the past decade. These enzymes, specifically, pyrroloquinoline quinone (PQQ)-bearing methanol dehydrogenases, efficiently convert alcohols to the respective aldehydes. To rationally design bioinspired alcohol dehydrogenation catalysts, it is imperative to understand the species involved in catalysis. However, given the extremely flexible coordination sphere of lanthanides, it is often difficult to assess the number and nature of the active species. Here, we show how such questions can be addressed by using a combination of ion mobility spectrometry, mass spectrometry, and quantum-chemical calculations to study the test systems PQQ and lanthanide-PQQ-crown ether ligand complexes. Specifically, we determine the gas-phase structures of [PQQH2]-, [PQQH2+H2O]-, [PQQH2+MeOH]-, [PQQ-15c5+H]+, and [PQQ-15c5+Ln+NO3]2+ (Ln = La to Lu, except Pm). In the latter case, a trend to smaller collision cross sections across the lanthanide series is clearly observable, in line with the well-known lanthanide contraction. We hope that in the future such investigations will help to guide the design and understanding of lanthanide-based biomimetic complexes optimized for catalytic function.
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Affiliation(s)
- Alexander Schäfer
- Karlsruhe Institute of Technology Institute of Physical Chemistry Fritz-Haber-Weg 2, 76128 Karlsruhe, Germany
| | - Violeta A Vetsova
- Department of Chemistry Ludwig Maximilian University of Munich Butenandtstraße 5-13, 81377 Munich, Germany
| | - Erik K Schneider
- Karlsruhe Institute of Technology Institute of Physical Chemistry Fritz-Haber-Weg 2, 76128 Karlsruhe, Germany
| | - Manfred Kappes
- Karlsruhe Institute of Technology Institute of Physical Chemistry Fritz-Haber-Weg 2, 76128 Karlsruhe, Germany
- Karlsruhe Institute of Technology Institute of Nanotechnology Hermann von Helmholtz Pl 1,76344 Eggenstein Leopoldshafen, Germany
| | - Michael Seitz
- University of Tübingen Institute of Inorganic Chemistry Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Lena J Daumann
- Department of Chemistry Ludwig Maximilian University of Munich Butenandtstraße 5-13, 81377 Munich, Germany
| | - Patrick Weis
- Karlsruhe Institute of Technology Institute of Physical Chemistry Fritz-Haber-Weg 2, 76128 Karlsruhe, Germany
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3
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Sarmiento-Pavía PD, Sosa-Torres ME. Bioinorganic insights of the PQQ-dependent alcohol dehydrogenases. J Biol Inorg Chem 2021; 26:177-203. [PMID: 33606117 DOI: 10.1007/s00775-021-01852-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/07/2021] [Indexed: 12/19/2022]
Abstract
Among the several alcohol dehydrogenases, PQQ-dependent enzymes are mainly found in the α, β, and γ-proteobacteria. These proteins are classified into three main groups. Type I ADHs are localized in the periplasm and contain one Ca2+-PQQ moiety, being the methanol dehydrogenase (MDH) the most representative. In recent years, several lanthanide-dependent MDHs have been discovered exploding the understanding of the natural role of lanthanide ions. Type II ADHs are localized in the periplasm and possess one Ca2+-PQQ moiety and one heme c group. Finally, type III ADHs are complexes of two or three subunits localized in the cytoplasmic membrane and possess one Ca2+-PQQ moiety and four heme c groups, and in one of these proteins, an additional [2Fe-2S] cluster has been discovered recently. From the bioinorganic point of view, PQQ-dependent alcohol dehydrogenases have been revived recently mainly due to the discovery of the lanthanide-dependent enzymes. Here, we review the three types of PQQ-dependent ADHs with special focus on their structural features and electron transfer processes. The PQQ-Alcohol dehydrogenases are classified into three main groups. Type I and type II ADHs are located in the periplasm, while type III ADHs are in the cytoplasmic membrane. ADH-I have a Ca-PQQ or a Ln-PQQ, ADH-II a Ca-PQQ and one heme-c and ADH-III a Ca-PQQ and four hemes-c. This review focuses on their structural features and electron transfer processes.
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Affiliation(s)
- Pedro D Sarmiento-Pavía
- Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, 04510, Ciudad de México, Mexico
| | - Martha E Sosa-Torres
- Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, 04510, Ciudad de México, Mexico.
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4
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The Effects of the Metal Ion Substitution into the Active Site of Metalloenzymes: A Theoretical Insight on Some Selected Cases. Catalysts 2020. [DOI: 10.3390/catal10091038] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A large number of enzymes need a metal ion to express their catalytic activity. Among the different roles that metal ions can play in the catalytic event, the most common are their ability to orient the substrate correctly for the reaction, to exchange electrons in redox reactions, to stabilize negative charges. In many reactions catalyzed by metal ions, they behave like the proton, essentially as Lewis acids but are often more effective than the proton because they can be present at high concentrations at neutral pH. In an attempt to adapt to drastic environmental conditions, enzymes can take advantage of the presence of many metal species in addition to those defined as native and still be active. In fact, today we know enzymes that contain essential bulk, trace, and ultra-trace elements. In this work, we report theoretical results obtained for three different enzymes each of which contains different metal ions, trying to highlight any differences in their working mechanism as a function of the replacement of the metal center at the active site.
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5
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Lumpe H, Daumann LJ. Studies of Redox Cofactor Pyrroloquinoline Quinone and Its Interaction with Lanthanides(III) and Calcium(II). Inorg Chem 2019; 58:8432-8441. [DOI: 10.1021/acs.inorgchem.9b00568] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Henning Lumpe
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Lena J. Daumann
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
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6
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Marino T, Prejanò M, Russo N. How Metal Coordination in the Ca-, Ce-, and Eu-Containing Methanol Dehydrogenase Enzymes Can Influence the Catalysis: A Theoretical Point of View. TRANSITION METALS IN COORDINATION ENVIRONMENTS 2019. [DOI: 10.1007/978-3-030-11714-6_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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7
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Lumpe H, Pol A, Op den Camp HJM, Daumann LJ. Impact of the lanthanide contraction on the activity of a lanthanide-dependent methanol dehydrogenase - a kinetic and DFT study. Dalton Trans 2018; 47:10463-10472. [PMID: 30020281 PMCID: PMC6085770 DOI: 10.1039/c8dt01238e] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/14/2018] [Indexed: 01/15/2023]
Abstract
Interest in the bioinorganic chemistry of lanthanides is growing rapidly as more and more lanthanide-dependent bacteria are being discovered. Especially the earlier lanthanides have been shown to be preferentially utilized by bacteria that need these Lewis acids as cofactors in their alcohol dehydrogenase enzymes. Here, we investigate the impact of the lanthanide ions lanthanum(iii) to lutetium(iii) (excluding Pm) on the catalytic parameters (vmax, KM, kcat/KM) of a methanol dehydrogenase (MDH) isolated from Methylacidiphilum fumariolicum SolV. Kinetic experiments and DFT calculations were used to discuss why only the earlier lanthanides (La-Gd) promote high MDH activity. Impact of Lewis acidity, coordination number preferences, stability constants and other properties that are a direct result of the lanthanide contraction are discussed in light of the two proposed mechanisms for MDH.
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Affiliation(s)
- Henning Lumpe
- Ludwig-Maximilians-Universität München
, Department Chemie
,
Butenandtstr. 5-13
, 81377 München
, Germany
.
| | - Arjan Pol
- Department of Microbiology
, Institute of Wetland and Water Research
, Radboud University Nijmegen
,
The Netherlands
| | - Huub J. M. Op den Camp
- Department of Microbiology
, Institute of Wetland and Water Research
, Radboud University Nijmegen
,
The Netherlands
| | - Lena J. Daumann
- Ludwig-Maximilians-Universität München
, Department Chemie
,
Butenandtstr. 5-13
, 81377 München
, Germany
.
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry
, Ludwig-Maximilians-Universität München
,
Germany
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8
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The crystal structure of methanol dehydrogenase, a quinoprotein from the marine methylotrophic bacterium Methylophaga aminisulfidivorans MPT. J Microbiol 2018; 56:246-254. [DOI: 10.1007/s12275-018-7483-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/11/2018] [Accepted: 01/15/2018] [Indexed: 10/17/2022]
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9
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McSkimming A, Cheisson T, Carroll PJ, Schelter EJ. Functional Synthetic Model for the Lanthanide-Dependent Quinoid Alcohol Dehydrogenase Active Site. J Am Chem Soc 2018; 140:1223-1226. [DOI: 10.1021/jacs.7b12318] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Alex McSkimming
- P. Roy and Diana T. Vagelos
Laboratories, Department of Chemistry, University of Pennsylvania, 231 S 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Thibault Cheisson
- P. Roy and Diana T. Vagelos
Laboratories, Department of Chemistry, University of Pennsylvania, 231 S 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Patrick J. Carroll
- P. Roy and Diana T. Vagelos
Laboratories, Department of Chemistry, University of Pennsylvania, 231 S 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Eric J. Schelter
- P. Roy and Diana T. Vagelos
Laboratories, Department of Chemistry, University of Pennsylvania, 231 S 34th Street, Philadelphia, Pennsylvania 19104, United States
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10
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Prejanò M, Marino T, Russo N. How Can Methanol Dehydrogenase from Methylacidiphilum fumariolicum
Work with the Alien CeIII
Ion in the Active Center? A Theoretical Study. Chemistry 2017; 23:8652-8657. [DOI: 10.1002/chem.201700381] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche; Università della Calabria; 87036 Arcavacata di Rende (CS) Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche; Università della Calabria; 87036 Arcavacata di Rende (CS) Italy
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche; Università della Calabria; 87036 Arcavacata di Rende (CS) Italy
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11
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12
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Wendlandt AE, Stahl SS. Quinone-Catalyzed Selective Oxidation of Organic Molecules. Angew Chem Int Ed Engl 2015; 54:14638-58. [PMID: 26530485 PMCID: PMC4859943 DOI: 10.1002/anie.201505017] [Citation(s) in RCA: 241] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Indexed: 01/12/2023]
Abstract
Quinones are common stoichiometric reagents in organic chemistry. Para-quinones with high reduction potentials, such as DDQ and chloranil, are widely used and typically promote hydride abstraction. In recent years, many catalytic applications of these methods have been achieved by using transition metals, electrochemistry, or O2 to regenerate the oxidized quinone in situ. Complementary studies have led to the development of a different class of quinones that resemble the ortho-quinone cofactors in copper amine oxidases and mediate the efficient and selective aerobic and/or electrochemical dehydrogenation of amines. The latter reactions typically proceed by electrophilic transamination and/or addition-elimination reaction mechanisms, rather than hydride abstraction pathways. The collective observations show that the quinone structure has a significant influence on the reaction mechanism and has important implications for the development of new quinone reagents and quinone-catalyzed transformations.
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Affiliation(s)
- Alison E Wendlandt
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706 (USA)
| | - Shannon S Stahl
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706 (USA).
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Wendlandt AE, Stahl SS. Chinon‐katalysierte, selektive Oxidation organischer Moleküle. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505017] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alison E. Wendlandt
- Department of Chemistry, University of Wisconsin‐Madison, 1101 University Avenue, Madison, Wisconsin 53706 (USA)
| | - Shannon S. Stahl
- Department of Chemistry, University of Wisconsin‐Madison, 1101 University Avenue, Madison, Wisconsin 53706 (USA)
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14
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Rozeboom HJ, Yu S, Mikkelsen R, Nikolaev I, Mulder HJ, Dijkstra BW. Crystal structure of quinone-dependent alcohol dehydrogenase from P
seudogluconobacter saccharoketogenes
. A versatile dehydrogenase oxidizing alcohols and carbohydrates. Protein Sci 2015; 24:2044-54. [DOI: 10.1002/pro.2818] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Henriëtte J. Rozeboom
- Laboratory of Biophysical Chemistry; Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen; Groningen The Netherlands
| | - Shukun Yu
- DuPont Industrial Biosciences; Brabrand, Aarhus Denmark
| | | | - Igor Nikolaev
- DuPont Industrial Biosciences; Leiden The Netherlands
| | | | - Bauke W. Dijkstra
- Laboratory of Biophysical Chemistry; Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen; Groningen The Netherlands
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Burbank KA, Walker RA, Peyton BM. A molecular level mechanism for uranium (VI) toxicity through Ca2+ displacement in pyrroloquinoline quinone-dependent bacterial dehydrogenase. J Inorg Biochem 2015; 149:59-67. [DOI: 10.1016/j.jinorgbio.2014.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 11/24/2014] [Accepted: 11/25/2014] [Indexed: 11/30/2022]
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Uchida W, Wakabayashi M, Ikemoto K, Nakano M, Ohtani H, Nakamura S. Mechanism of glycine oxidation catalyzed by pyrroloquinoline quinone in aqueous solution. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.12.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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17
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Li T, Yan Y, He J. Enhanced direct fermentation of cassava to butanol by Clostridium species strain BOH3 in cofactor-mediated medium. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:166. [PMID: 26464582 PMCID: PMC4603972 DOI: 10.1186/s13068-015-0351-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 09/30/2015] [Indexed: 05/07/2023]
Abstract
BACKGROUND The main challenge of cassava-based biobutanol production is to enhance the simultaneous saccharification and fermentation with high hyperamylolytic activity and butanol yield. Manipulation of cofactor [e.g., Ca(2+) and NAD/(P)H] levels as a potential tool to modulate carbon flux plays a key role in the cassava hydrolysis capacity and butanol productivity. Here, we aimed to develop a technology for enhancing butanol production with simultaneous hydrolysis of cassava (a typical model as a non-cereal starchy material) using a cofactor-dependent modulation method to maximize the production efficacy of biobutanol by Clostridium sp. stain BOH3. RESULTS Supplementing CaCO3 to the medium containing cassava significantly promotes activities of α-amylase responsible for cassava hydrolysis and butanol production due to the role of Ca(2+) cofactor-dependent pathway in conversion of cassava starch to reducing sugar and its buffering capacity. Also, after applying redox modulation with l-tryptophan (a precursor as de novo synthesis of NADH and NADPH), the levels of cofactor NADH and NADPH increased significantly by 67 % in the native cofactor-dependent system of the wild-type Clostridium sp. stain BOH3. Increasing availability of NADH and NADPH improved activities of NADH- and NADPH-dependent butanol dehydrogenases, and thus could selectively open the valve of carbon flux toward the more reduced product, butanol, against the more oxidized acid or acetone products. By combining CaCO3 and l-tryptophan, 17.8 g/L butanol with a yield of 30 % and a productivity of 0.25 g/L h was obtained with a hydrolytic capacity of 88 % towards cassava in a defined medium. The metabolic patterns were shifted towards more reduced metabolites as reflected by higher butanol-acetone ratio (76 %) and butanol-bioacid ratio (500 %). CONCLUSIONS The strategy of altering enzyme cofactor supply may provide an alternative tool to enhance the stimulation of saccharification and fermentation in a cofactor-dependent production system. While genetic engineering focuses on strain improvement to enhance butanol production, cofactor technology can fully exploit the productivity of a strain and maximize the production efficiency.
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Affiliation(s)
- Tinggang Li
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, Singapore, 117576 Singapore
| | - Yu Yan
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, Singapore, 117576 Singapore
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, Singapore, 117576 Singapore
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18
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Bogart JA, Lewis AJ, Schelter EJ. DFT study of the active site of the XoxF-type natural, cerium-dependent methanol dehydrogenase enzyme. Chemistry 2014; 21:1743-8. [PMID: 25421364 DOI: 10.1002/chem.201405159] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Indexed: 11/07/2022]
Abstract
Rare-earth metal cations have recently been demonstrated to be essential co-factors for the growth of the methanotrophic bacterium Methylacidiphilum fumariolicum SolV. A crystal structure of the rare-earth-dependent methanol dehydrogenase (MDH) includes a cerium cation in the active site. Herein, the Ce-MDH active site has been analyzed through DFT calculations. The results show the stability of the Ce(III)-pyrroloquinoline quinone (PQQ) semiquinone configuration. Calculations on the active oxidized form of this complex indicate a 0.81 eV stabilization of the PQQ(0) LUMO at cerium versus calcium, supporting the observation that the cerium cation in the active site confers a competitive advantage to Methylacidiphilum fumariolicum SolV. Using reported aqueous electrochemical data, a semi-empirical correlation was established based on cerium(IV/III) redox potentials. The correlation allowed estimation of the cerium oxidation potential of +1.35 V versus saturated calomel electrode (SCE) in the active site. The results are expected to guide the design of functional model complexes and alcohol-oxidation catalysts based on lanthanide complexes of biologically relevant quinones.
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Affiliation(s)
- Justin A Bogart
- Department of Chemistry, University of Pennsylvania, P. Roy and Diana T. Vagelos Laboratories, Philadlephia, PA 19104 (USA)
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19
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Biological conversion of methane to liquid fuels: status and opportunities. Biotechnol Adv 2014; 32:1460-75. [PMID: 25281583 DOI: 10.1016/j.biotechadv.2014.09.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 09/01/2014] [Accepted: 09/24/2014] [Indexed: 12/21/2022]
Abstract
Methane is the main component of natural gas and biogas. As an abundant energy source, methane is crucial not only to meet current energy needs but also to achieve a sustainable energy future. Conversion of methane to liquid fuels provides energy-dense products and therefore reduces costs for storage, transportation, and distribution. Compared to thermochemical processes, biological conversion has advantages such as high conversion efficiency and using environmentally friendly processes. This paper is a comprehensive review of studies on three promising groups of microorganisms (methanotrophs, ammonia-oxidizing bacteria, and acetogens) that hold potential in converting methane to liquid fuels; their habitats, biochemical conversion mechanisms, performance in liquid fuels production, and genetic modification to enhance the conversion are also discussed. To date, methane-to-methanol conversion efficiencies (moles of methanol produced per mole methane consumed) of up to 80% have been reported. A number of issues that impede scale-up of this technology, such as mass transfer limitations of methane, inhibitory effects of H2S in biogas, usage of expensive chemicals as electron donors, and lack of native strains capable of converting methane to liquid fuels other than methanol, are discussed. Future perspectives and strategies in addressing these challenges are also discussed.
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20
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VanEngelen MR, Szilagyi RK, Gerlach R, Lee BD, Apel WA, Peyton BM. Uranium exerts acute toxicity by binding to pyrroloquinoline quinone cofactor. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:937-942. [PMID: 21166389 DOI: 10.1021/es101754x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Uranium as an environmental contaminant has been shown to be toxic to eukaryotes and prokaryotes; however, no specific mechanisms of uranium toxicity have been proposed so far. Here a combination of in vivo, in vitro, and in silico studies are presented describing direct inhibition of pyrroloquinoline quinone (PQQ)-dependent growth and metabolism by uranyl cations. Electrospray-ionization mass spectroscopy, UV-vis optical spectroscopy, competitive Ca(2+)/uranyl binding studies, relevant crystal structures, and molecular modeling unequivocally indicate the preferred binding of uranyl simultaneously to the carboxyl oxygen, pyridine nitrogen, and quinone oxygen of the PQQ molecule. The observed toxicity patterns are consistent with the biotic ligand model of acute metal toxicity. In addition to the environmental implications, this work represents the first proposed molecular mechanism of uranium toxicity in bacteria, and has relevance for uranium toxicity in many living systems.
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Affiliation(s)
- Michael R VanEngelen
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana 59717-3920, United States
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Hothi P, Sutcliffe M, Scrutton N. Kinetic isotope effects and ligand binding in PQQ-dependent methanol dehydrogenase. Biochem J 2009; 388:123-33. [PMID: 15617516 PMCID: PMC1186700 DOI: 10.1042/bj20041731] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The reaction of PQQ (2,7,9-tricarboxypyrroloquinoline quinone)-dependent MDH (methanol dehydrogenase) from Methylophilus methylotrophus has been studied under steady-state conditions in the presence of an alternative activator [GEE (glycine ethyl ester)] and compared with similar reactions performed with ammonium (used more generally as an activator in steady-state analysis of MDH). Studies of initial velocity with methanol (protiated methanol, C1H3O1H) and [2H]methanol (deuteriated methanol, C2H3O2H) as substrate, performed with different concentrations of GEE and PES (phenazine ethosulphate), indicate competitive binding effects for substrate and PES on the stimulation and inhibition of enzyme activity by GEE. GEE is more effective at stimulating activity than ammonium at low concentrations, suggesting tighter binding of GEE to the active site. Inhibition of activity at high GEE concentration is less pronounced than at high ammonium concentration. This suggests a close spatial relationship between the stimulatory (KS) and inhibitory (KI) binding sites in that binding of GEE to the KS site sterically impairs the binding of GEE to the KI site. The binding of GEE is also competitive with the binding of PES, and GEE is more effective than ammonium in competing with PES. This competitive binding of GEE and PES lowers the effective concentration of PES at the site competent for electron transfer. Accordingly, the oxidative half-reaction, which is second-order with respect to PES concentration, is more rate-limiting in steady-state turnover with GEE than with ammonium. The smaller methanol C-1H/C-2H kinetic isotope effects observed with GEE are consistent with a larger contribution made by the oxidative half-reaction to rate limitation. Cyanide is much less effective at suppressing 'endogenous' activity in the presence of GEE than with ammonium, which is attributed to impaired binding of cyanide to the catalytic site through steric interaction with GEE bound at the KS site. The kinetic model developed previously for reactions of MDH with ammonium [Hothi, Basran, Sutcliffe and Scrutton (2003) Biochemistry 42, 3966-3978] is consistent with data obtained with GEE, although a more detailed structural interpretation is given here. Molecular-modelling studies rationalize the kinetic observations in terms of a complex binding scenario at the molecular level involving two spatially distinct inhibitory sites (KI and KI'). The KI' site caps the entrance to the active site and is interpreted as the PES binding site. The KI site is adjacent to, and, for GEE, overlaps with, the KS site, and is located in the active-site cavity close to the PQQ cofactor and the catalytic site for methanol oxidation.
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Affiliation(s)
- Parvinder Hothi
- *Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
| | - Michael J. Sutcliffe
- *Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
- †Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
| | - Nigel S. Scrutton
- *Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
- To whom correspondence should be addressed (email )
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Machado SS, Jongejan A, Geerlof A, Jongejan JA, Duine JA. Entropic And Enthalpic Contributions To The Enantioselectivity Of Quinohaemoprotein Alcohol Dehydrogenases FromAcetobacter PasteurianusAndComamonas TestosteroniIn The Oxidation Of Primary And Secondary Alcohols. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.3109/10242429909040114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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23
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Idupulapati N, Mainardi D. Coordination and binding of ions in Ca2+- and Ba2+-containing methanol dehydrogenase and interactions with methanol. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Leopoldini M, Russo N, Toscano M. The Preferred Reaction Path for the Oxidation of Methanol by PQQ-Containing Methanol Dehydrogenase: Addition–Elimination versus Hydride-Transfer Mechanism. Chemistry 2007; 13:2109-17. [PMID: 17149777 DOI: 10.1002/chem.200601123] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The catalytic oxidation of methanol to formaldehyde by pyrroloquinoline quinone (PQQ)-containing methanol dehydrogenase (MDH) was investigated at density functional B3LYP level. The still controversial addition-elimination and hydride-transfer reaction mechanisms were analysed. Computations performed in the gas phase and in the protein environment indicated that both suggested reaction sequences involve very high activation barriers. In this situation, the reactions should have scarce probability to occur and the preference for one of the two paths cannot be stated. Here, we will show how some corrections to the successive steps in the addition-elimination mechanism can sensibly decrease the activation barriers height, making possible the determination of the MDH-preferred catalytic path.
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Affiliation(s)
- Monica Leopoldini
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni, Parallele e Distribuite-Centro d'Eccellenza MIUR, Universita' della Calabria, 87030 Arcavacata di Rende (CS), Italy
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25
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Zhang X, Reddy SY, Bruice TC. Mechanism of methanol oxidation by quinoprotein methanol dehydrogenase. Proc Natl Acad Sci U S A 2007; 104:745-9. [PMID: 17215371 PMCID: PMC3020142 DOI: 10.1073/pnas.0610126104] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
At neutral pH, oxidation of CH(3)OH --> CH(2)O by an o-quinone requires general-base catalysis and the reaction is endothermic. The active-site -CO(2)(-) groups of Glu-171 and Asp-297 (Glu-171-CO(2)(-) and Asp-297-CO(2)(-)) have been considered as the required general base catalysts in the bacterial o-quinoprotein methanol dehydrogenase (MDH) reaction. Based on quantum mechanics/molecular mechanics (QM/MM) calculations, the free energy for MeOH reduction of o-PQQ when MeOH is hydrogen bonded to Glu-171-CO(2)(-) and the crystal water (Wat1) is hydrogen bonded to Asp-297-CO(2)(-) is DeltaG++ = 11.7 kcal/mol, which is comparable with the experimental value of 8.5 kcal/mol. The calculated DeltaG++ when MeOH is hydrogen bonded to Asp-297-CO(2)(-) is >50 kcal/mol. The Asp-297-CO(2)(-)...Wat1 complex is very stable. Molecular dynamics (MD) simulations on MDH.PQQ.Wat1 complex in TIP3P water for 5 ns does not result in interchange of Asp-297-CO(2)(-) bound Wat1 for a solvent water. Starting with Wat1 removed and MeOH hydrogen bonded to Asp-297-CO(2)(-), we find that MeOH returns to be hydrogen bonded to Glu-171-CO(2)(-) and Asp-297-CO(2)(-) coordinates to Ca(2+) during 3 ns simulation. The Asp-297-CO(2)(-)...Wat1 of reactant complex does play a crucial role in catalysis. By QM/MM calculation DeltaG++ = 1.1 kcal/mol for Asp-297-CO(2)(-) general-base catalysis of Wat1 hydration of the immediate CH(2)==O product --> CH(2)(OH)(2). By this means, the endothermic oxidation-reduction reaction is pulled such that the overall conversion of MeOH to CH(2)(OH)(2) is exothermic.
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Affiliation(s)
- Xiaodong Zhang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106
| | - Swarnalatha Y. Reddy
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106
| | - Thomas C. Bruice
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106
- *To whom correspondence should be addressed. E-mail:
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26
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Kay CWM, Mennenga B, Görisch H, Bittl R. Structure of the Pyrroloquinoline Quinone Radical in Quinoprotein Ethanol Dehydrogenase. J Biol Chem 2006; 281:1470-6. [PMID: 16267040 DOI: 10.1074/jbc.m511132200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Quinoprotein alcohol dehydrogenases use the pyrroloquinoline quinone (PQQ) cofactor to catalyze the oxidation of alcohols. The catalytic cycle is thought to involve a hydride transfer from the alcohol to the oxidized PQQ, resulting in the generation of aldehyde and reduced PQQ. Reoxidation of the cofactor by cytochrome proceeds in two sequential steps via the PQQ radical. We have used a combination of electron nuclear double resonance and density functional theory to show that the PQQ radical is not protonated at either O-4 or O-5, a result that is at variance with the general presumption of a singly protonated radical. The quantum mechanical calculations also show that reduced PQQ is unlikely to be protonated at O-5; rather, it is either singly protonated at O-4 or not protonated at either O-4 or O-5, a result that also challenges the common assumption of a reduced PQQ protonated at both O-4 and O-5. The reaction cycle of PQQ-dependent alcohol dehydrogenases is revised in light of these findings.
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Affiliation(s)
- Christopher W M Kay
- Institut für Experimentalphysik, Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany.
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27
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Reddy SY, Bruice TC. Determination of enzyme mechanisms by molecular dynamics: studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase. Protein Sci 2005; 13:1965-78. [PMID: 15273299 PMCID: PMC2279812 DOI: 10.1110/ps.04673404] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Molecular dynamics (MD) simulations have been carried out to study the enzymatic mechanisms of quinoproteins, methanol dehydrogenase (MDH), and soluble glucose dehydrogenase (sGDH). The mechanisms of reduction of the orthoquinone cofactor (PQQ) of MDH and sGDH involve concerted base-catalyzed proton abstraction from the hydroxyl moiety of methanol or from the 1-hydroxyl of glucose, and hydride equivalent transfer from the substrate to the quinone carbonyl carbon C5 of PQQ. The products of methanol and glucose oxidation are formaldehyde and glucolactone, respectively. The immediate product of PQQ reduction, PQQH- [-HC5(O-)-C4(=O)-] and PQQH [-HC5(OH)-C4(=O)-] converts to the hydroquinone PQQH2 [-C5(OH)=C4(OH)-]. The main focus is on MD structures of MDH * PQQ * methanol, MDH * PQQH-, MDH * PQQH, sGDH * PQQ * glucose, sGDH * PQQH- (glucolactone, and sGDH * PQQH. The reaction PQQ-->PQQH- occurs with Glu 171-CO2- and His 144-Im as the base species in MDH and sGDH, respectively. The general-base-catalyzed hydroxyl proton abstraction from substrate concerted with hydride transfer to the C5 of PQQ is assisted by hydrogen-bonding to the C5=O by Wat1 and Arg 324 in MDH and by Wat89 and Arg 228 in sGDH. Asp 297-COOH would act as a proton donor for the reaction PQQH(-)-->PQQH, if formed by transfer of the proton from Glu 171-COOH to Asp 297-CO2- in MDH. For PQQH-->PQQH2, migration of H5 to the C4 oxygen may be assisted by a weak base like water (either by crystal water Wat97 or bulk solvent, hydrogen-bonded to Glu 171-CO2- in MDH and by Wat89 in sGDH).
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Affiliation(s)
- Swarnalatha Y Reddy
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
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28
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Masgrau L, Basran J, Hothi P, Sutcliffe MJ, Scrutton NS. Hydrogen tunneling in quinoproteins. Arch Biochem Biophys 2004; 428:41-51. [PMID: 15234268 DOI: 10.1016/j.abb.2004.03.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2004] [Revised: 03/15/2004] [Indexed: 10/26/2022]
Abstract
It is now widely accepted that substrate C-H bond breakage by quinoprotein enzymes occurs by quantum mechanical tunneling. This paradigm shift in the conceptual framework for these reactions away from semi-classical transition state theory (i.e., including zero-point energy but with no tunneling correction) has been driven over recent years by experimental studies of the temperature dependence of kinetic isotope effects for these reactions in the TTQ-dependent enzymes methylamine dehydrogenase and aromatic amine dehydrogenase, which produced observations also inconsistent with the simple Bell correction model of tunneling. However, these data-specifically, the strong temperature dependence of reaction rates and the variable temperature dependence of kinetic isotope effects-are consistent with other tunneling models (denoted full tunneling models) in which protein and/or substrate fluctuations generate a configuration compatible with tunneling. These models accommodate substrate/protein (environment) fluctuations required to attain a configuration with degenerate quantum states and, when necessary, motion required to increase the probability of tunneling in these states. Furthermore, tunneling mechanisms in quinoproteins are supported by computational studies employing variational transition state theory with multidimensional tunneling corrections; these studies are also discussed in this review. Potential pitfalls in analyzing the temperature dependence of kinetic isotope effects as probes of tunneling are also discussed with reference to PQQ-dependent methanol dehydrogenase.
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Affiliation(s)
- Laura Masgrau
- Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, UK
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29
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Kay CWM, Mennenga B, Görisch H, Bittl R. Characterisation of the PQQ cofactor radical in quinoprotein ethanol dehydrogenase of Pseudomonas aeruginosa by electron paramagnetic resonance spectroscopy. FEBS Lett 2004; 564:69-72. [PMID: 15094044 DOI: 10.1016/s0014-5793(04)00317-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2004] [Revised: 03/09/2004] [Accepted: 03/12/2004] [Indexed: 11/22/2022]
Abstract
The binding pocket of the pyrroloquinoline quinone (PQQ) cofactor in quinoprotein alcohol dehydrogenases contains a characteristic disulphide ring formed by two adjacent cysteine residues. To analyse the function of this unusual structural motif we have investigated the wild-type and a double cysteine:alanine mutant of the quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa by electron paramagnetic resonance (EPR) spectroscopy. Thus, we have obtained the principal values for the full rhombic g-tensor of the PQQ semiquinone radical by high-field (94 GHz) EPR necessary for a discrimination of radical species in dehydrogenases containing PQQ together with other redox-active cofactors. Our results show that the characteristic disulphide ring is no prerequisite for the formation of the functionally important semiquinone form of PQQ.
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Affiliation(s)
- Christopher W M Kay
- Institut für Experimentalphysik, Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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30
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Reddy SY, Bruice TC. Mechanism of Glucose Oxidation by Quinoprotein Soluble Glucose Dehydrogenase: Insights from Molecular Dynamics Studies. J Am Chem Soc 2004; 126:2431-8. [PMID: 14982451 DOI: 10.1021/ja039722r] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have generated 3 ns molecular dynamic (MD) simulations, in aqueous solution, of the bacterial soluble glucose dehydrogenase enzyme.PQQ.glucose complex and intermediates formed in PQQ reduction. In the MD structure of enzyme.PQQ.glucose complex the imidazole of His144 is hydrogen bonded to the hydroxyl hydrogen of H[bond]OC1(H) of glucose. The tightly hydrogen-bonded triad Asp163-His144-glucose (2.70 and 2.91 A) is involved in proton abstraction from glucose concerted with the hydride transfer from the C1[bond]H of glucose to the >C5[double bond]O quinone carbon of PQQ. The reaction is assisted by Arg228 hydrogen bonding to the carbonyl oxygen of >C5[double bond]O. The rearrangement of [bond](H)C5(O-)[bond]C4([double bond]O)[bond] of II to [bond]C5(OH)[double bond]C4(OH)[bond] of PQQH(2) hydroquinone is assisted by general acid protonatation of the >C4[double bond]O oxygen by protonated His144 and hydrogen bonds of Arg228 to the oxyanion O5. The continuous hydrogen bonding of the amide side chain of Asn229 to >C4[double bond]O4 oxygen and that of the O5 oxygen of the cofactor to Wat89 is observed throughout the entire reaction.
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Affiliation(s)
- Swarnalatha Y Reddy
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
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31
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Reddy SY, Bruice TC. In silico studies of the mechanism of methanol oxidation by quinoprotein methanol dehydrogenase. J Am Chem Soc 2003; 125:8141-50. [PMID: 12837084 DOI: 10.1021/ja034406y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism of bacterial methanol dehydrogenase involves hydride equivalent transfer from substrate to the ortho-quinone PQQ to provide a C5-reduced intermediate that subsequently rearranges to the hydroquinone PQQH(2). We have studied the PQQ reduction by molecular dynamic (MD) simulations in aqueous solution. Among the five simulated structures, either Asp297 or Glu171 or both are ionized. Reasonable structures are obtained only when both carboxyl groups are ionized. This is not unexpected since the kinetic pH optimum is 9.0. In the structure of the enzyme.PQQ.HOCH(3) complex, the hydrogen bonded Glu171-CO(2)(-).H-OCH(3) is in a position to act as a general base catalyst for hydride equivalent transfer to C5 of PQQ. We thus suggest that Glu171 plays the role of general base catalyst in PQQ reduction rather than Asp297 as previously suggested. The reduction is assisted by Arg324, which hydrogen bonds to the ortho-quinone moiety of PQQ. The rearrangement of the C5-reduced intermediate to provide hydroquinone PQQH(2) is also assisted by proton abstraction by Glu171-CO(2)(-) and the continuous hydrogen bonding of Arg324 throughout the entire reaction. These features as well as the mapping of the channel for substrate and water into the active site entrance are the observations of major importance.
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Affiliation(s)
- Swarnalatha Y Reddy
- Department of Chemistry and Biochemistry, University of California-Santa Barbara, Santa Barbara, CA 93106, USA
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32
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Reddy SY, Mathews F, Zheng YJ, Bruice TC. Quinoprotein methanol dehydrogenase: a molecular dynamics study and comparison with crystal structure. J Mol Struct 2003. [DOI: 10.1016/s0022-2860(03)00257-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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33
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Oubrie A. Structure and mechanism of soluble glucose dehydrogenase and other PQQ-dependent enzymes. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1647:143-51. [PMID: 12686124 DOI: 10.1016/s1570-9639(03)00087-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
This paper discusses recent X-ray structures of several pyrroloquinoline quinone (PQQ)-dependent proteins in relation to their proposed modes of action. In addition, a detailed analysis of redox-related structural changes in the soluble PQQ-dependent glucose dehydrogenase is presented. A sequence comparison of that enzyme with a number of homologues shows that PQQ-dependent enzymes are much more widespread than has been assumed so far. In particular, the presence of a PQQ-dependent enzyme in at least one archaeon opens up the possibility that PQQ has been involved in prokaryotic metabolism since the early days of the evolution of bacterial life on earth.
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Affiliation(s)
- Arthur Oubrie
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
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34
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Chen ZW, Matsushita K, Yamashita T, Fujii TA, Toyama H, Adachi O, Bellamy HD, Mathews FS. Structure at 1.9 A resolution of a quinohemoprotein alcohol dehydrogenase from Pseudomonas putida HK5. Structure 2002; 10:837-49. [PMID: 12057198 DOI: 10.1016/s0969-2126(02)00774-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The type II quinohemoprotein alcohol dehydrogenase of Pseudomonas putida is a periplasmic enzyme that oxidizes substrate alcohols to the aldehyde and transfers electrons first to pyrroloquinoline quinone (PQQ) and then to an internal heme group. The 1.9 A resolution crystal structure reveals that the enzyme contains a large N-terminal eight-stranded beta propeller domain (approximately 60 kDa) similar to methanol dehydrogenase and a small C-terminal c-type cytochrome domain (approximately 10 kDa) similar to the cytochrome subunit of p-cresol methylhydoxylase. The PQQ is bound near the axis of the propeller domain about 14 A from the heme. A molecule of acetone, the product of the oxidation of isopropanol present during crystallization, appears to be bound in the active site cavity.
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Affiliation(s)
- Zhi-wei Chen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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35
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Jongejan A, Jongejan JA, Hagen WR. Direct hydride transfer in the reaction mechanism of quinoprotein alcohol dehydrogenases: a quantum mechanical investigation. J Comput Chem 2001; 22:1732-1749. [PMID: 12116408 DOI: 10.1002/jcc.1128] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Oxidation of alcohols by direct hydride transfer to the pyrroloquinoline quinone (PQQ) cofactor of quinoprotein alcohol dehydrogenases has been studied using ab initio quantum mechanical methods. Energies and geometries were calculated at the 6-31G(d,p) level of theory. Comparison of the results obtained for PQQ and several derivatives with available structural and spectroscopic data served to judge the feasibility of the calculations. The role of calcium in the enzymatic reaction mechanism has been investigated. Transition state searches have been conducted at the semiempirical and STO-3G(d) level of theory. It is concluded that hydride transfer from the Calpha-position of the substrate alcohol (or aldehyde) directly to the C(5) carbon of PQQ is energetically feasible. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1732-1749, 2001
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Affiliation(s)
- A. Jongejan
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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36
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Affiliation(s)
- C Anthony
- Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Southampton SO16 7PX
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37
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Vangnai AS, Arp DJ. An inducible 1-butanol dehydrogenase, a quinohaemoprotein, is involved in the oxidation of butane by "Pseudomonas butanovora". MICROBIOLOGY (READING, ENGLAND) 2001; 147:745-756. [PMID: 11238982 DOI: 10.1099/00221287-147-3-745] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Butane-grown "Pseudomonas butanovora" expressed two soluble alcohol dehydrogenases (ADHs), an NAD(+)-dependent secondary ADH and an NAD(+)-independent primary ADH. Two additional NAD(+)-dependent secondary ADHs could be detected when cells were grown on 2-butanol and lactate. The inducible NAD(+)-independent 1-butanol dehydrogenase (BDH) of butane-grown cells was primarily responsible for 1-butanol oxidation in the butane metabolism pathway. BDH was purified to near homogeneity and identified as a quinohaemoprotein, containing, per mol enzyme, 1.0 mol pyrroloquinoline quinone (PQQ) and 0.25 mol haem c as prosthetic groups. BDH was synthesized as a monomer of approximately 66 kDa. It has a broad substrate range, including primary alcohols, secondary alcohols, aldehydes, C(4) diols and aromatic alcohols. It exhibited the lowest K:(m) (7+/-1 microM) and highest k(cat)/K:(m) (72x10(4) M(-1) s(-1)) value towards 1-butanol. BDH exhibited ferricyanide-dependent ADH activity. Calcium ions (up to 10 mM) increased BDH activity substantially. Two BDH internal amino acid sequences showed 73 and 62% identity and 83 and 66% similarity, respectively, when compared with an amino acid sequence of ethanol dehydrogenase from Comamonas testosteroni. The presence of the inducible BDH and secondary ADH may indicate that the terminal and subterminal oxidation pathways are involved in butane degradation of butane-grown "P. butanovora".
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Affiliation(s)
- Alisa S Vangnai
- Department of Biochemistry and Biophysics, Laboratory for Nitrogen Fixation Research1, and Department of Botany and Plant Pathology2, Oregon State University, Cordley 2082, Corvallis, 97331-2902 OR, USA
| | - Daniel J Arp
- Department of Biochemistry and Biophysics, Laboratory for Nitrogen Fixation Research1, and Department of Botany and Plant Pathology2, Oregon State University, Cordley 2082, Corvallis, 97331-2902 OR, USA
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38
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Zheng YJ, Mathews FS, Bruice TC. Catalytic mechanism of quinoprotein methanol dehydrogenase: A theoretical and x-ray crystallographic investigation. Proc Natl Acad Sci U S A 2001; 98:432-4. [PMID: 11149955 PMCID: PMC14603 DOI: 10.1073/pnas.98.2.432] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The catalytic mechanism of the reductive half reaction of the quinoprotein methanol dehydrogenase (MDH) is believed to proceed either through a hemiketal intermediate or by direct transfer of a hydride ion from the substrate methyl group to the cofactor, pyrroloquinoline quinone (PQQ). A crystal structure of the enzyme-substrate complex of a similar quinoprotein, glucose dehydrogenase, has recently been reported that strongly favors the hydride transfer mechanism in that enzyme. A theoretical analysis and an improved refinement of the 1.9-A resolution crystal structure of MDH from Methylophilus methylotrophus W3A1 in the presence of methanol, reported earlier, indicates that the observed tetrahedral configuration of the C-5 atom of PQQ in that study represents the C-5-reduced form of the cofactor and lends support for a hydride transfer mechanism for MDH.
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Affiliation(s)
- Y J Zheng
- DuPont Agriculture Products, Stine-Haskell Research Center, Newark, DE 19714, USA
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39
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Catalytic mechanism of quinoprotein methanol dehydrogenase: A theoretical and x-ray crystallographic investigation. Proc Natl Acad Sci U S A 2001. [PMID: 11149955 PMCID: PMC14603 DOI: 10.1073/pnas.021547498] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The catalytic mechanism of the reductive half reaction of the quinoprotein methanol dehydrogenase (MDH) is believed to proceed either through a hemiketal intermediate or by direct transfer of a hydride ion from the substrate methyl group to the cofactor, pyrroloquinoline quinone (PQQ). A crystal structure of the enzyme-substrate complex of a similar quinoprotein, glucose dehydrogenase, has recently been reported that strongly favors the hydride transfer mechanism in that enzyme. A theoretical analysis and an improved refinement of the 1.9-A resolution crystal structure of MDH from Methylophilus methylotrophus W3A1 in the presence of methanol, reported earlier, indicates that the observed tetrahedral configuration of the C-5 atom of PQQ in that study represents the C-5-reduced form of the cofactor and lends support for a hydride transfer mechanism for MDH.
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Zhao Y, Wang G, Cao Z, Wang Y, Cheng H, Zhou HM. Effects of Ca2+ on the activity and stability of methanol dehydrogenase. JOURNAL OF PROTEIN CHEMISTRY 2000; 19:469-73. [PMID: 11195971 DOI: 10.1023/a:1026597314542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The effects of exogenously added Ca2+ on the enzymatic activity and structural stability of methanol dehydrogenase were studied for various Ca2+ concentrations. Methanol dehydrogenase activity increased significantly with increasing concentration of Ca2+, approaching saturation at 200 mM Ca2+. The effect of Ca2+ on the activation of MDH was time dependent and Ca2+ specific and was due to binding of the metal ions to the enzyme. Addition of increasing concentration of Ca2+ caused a decrease of the intrinsic tryptophan fluorescence intensity in a concentration-dependent manner to a minimum at 200 mM, but with no change in the fluorescence emission maximum wavelength or the CD spectra. The results revealed that the activation of methanol dehydrogenase by Ca2+ occurred concurrently with the conformational change. In addition, exogenously bound Ca2+ destabilized MDH. The potential biological significance of these results is discussed.
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Affiliation(s)
- Y Zhao
- Department of Biochemistry and Biophysics, College of Life Scineces, Wuhan University, China
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Oubrie A, Dijkstra BW. Structural requirements of pyrroloquinoline quinone dependent enzymatic reactions. Protein Sci 2000; 9:1265-73. [PMID: 10933491 PMCID: PMC2144678 DOI: 10.1110/ps.9.7.1265] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
On the basis of crystal structures of the pyrroloquinoline quinone (PQQ) dependent enzymes methanol dehydrogenase (MDH) and soluble glucose dehydrogenase (s-GDH), different catalytic mechanisms have been proposed. However, several lines of biochemical and kinetic evidence are strikingly similar for both enzymes. To resolve this discrepancy, we have compared the structures of these enzymes in complex with their natural substrates in an attempt to bring them in line with a single reaction mechanism. In both proteins, PQQ is located in the center of the molecule near the axis of pseudo-symmetry. In spite of the absence of significant sequence homology, the overall binding of PQQ in the respective active sites is similar. Hydrogen bonding interactions are made with polar protein side chains in the plane of the cofactor, whereas hydrophobic stacking interactions are important below and above PQQ. One Arg side chain and one calcium ion are ligated to the ortho-quinone group of PQQ in an identical fashion in either active site, in agreement with their proposed catalytic function of polarizing the PQQ C5-O5 bond. The substrates are bound in a similar position above PQQ and within hydrogen bond distance of the putative general bases Asp297 (MDH) and His144 (s-GDH). On the basis of these similarities, we propose that MDH and s-GDH react with their substrates through an identical mechanism, comprising general base-catalyzed hydride transfer from the substrate to PQQ and subsequent tautomerization of the PQQ intermediate to reduced PQQ.
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Affiliation(s)
- A Oubrie
- Laboratory of Biophysical Chemistry and BIOSON Research Institute, University of Groningen, The Netherlands
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Keitel T, Diehl A, Knaute T, Stezowski JJ, Höhne W, Görisch H. X-ray structure of the quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa: basis of substrate specificity. J Mol Biol 2000; 297:961-74. [PMID: 10736230 DOI: 10.1006/jmbi.2000.3603] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The homodimeric enzyme form of quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa ATCC 17933 crystallizes readily with the space group R3. The X-ray structure was solved at 2.6 A resolution by molecular replacement. Aside from differences in some loops, the folding of the enzyme is very similar to the large subunit of the quinoprotein methanol dehydrogenases from Methylobacterium extorquens or Methylophilus W3A1. Eight W-shaped beta-sheet motifs are arranged circularly in a propeller-like fashion forming a disk-shaped superbarrel. No electron density for a small subunit like that in methanol dehydrogenase could be found. The prosthetic group is located in the centre of the superbarrel and is coordinated to a calcium ion. Most amino acid residues found in close contact with the prosthetic group pyrroloquinoline quinone and the Ca(2+) are conserved between the quinoprotein ethanol dehydrogenase structure and that of the methanol dehydrogenases. The main differences in the active-site region are a bulky tryptophan residue in the active-site cavity of methanol dehydrogenase, which is replaced by a phenylalanine and a leucine side-chain in the ethanol dehydrogenase structure and a leucine residue right above the pyrrolquinoline quinone group in methanol dehydrogenase which is replaced by a tryptophan side-chain. Both amino acid exchanges appear to have an important influence, causing different substrate specificities of these otherwise very similar enzymes. In addition to the Ca(2+) in the active-site cavity found also in methanol dehydrogenase, ethanol dehydrogenase contains a second Ca(2+)-binding site at the N terminus, which contributes to the stability of the native enzyme.
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Affiliation(s)
- T Keitel
- Universitätsklinikum Charité Institut für Biochemie, Humboldt-Universität zu Berlin, Monbijoustr. 2, Berlin, D-10117, Germany
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Jongejan A, Machado SS, Jongejan JA. The enantioselectivity of quinohaemoprotein alcohol dehydrogenases: mechanistic and structural aspects. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1381-1177(99)00063-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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44
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Itoh S, Kawakami H, Fukuzumi S. Development of the active site model for calcium-containing quinoprotein alcohol dehydrogenases. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1381-1177(99)00070-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Oubrie A, Rozeboom HJ, Dijkstra BW. Active-site structure of the soluble quinoprotein glucose dehydrogenase complexed with methylhydrazine: a covalent cofactor-inhibitor complex. Proc Natl Acad Sci U S A 1999; 96:11787-91. [PMID: 10518528 PMCID: PMC18364 DOI: 10.1073/pnas.96.21.11787] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Soluble glucose dehydrogenase (s-GDH) from the bacterium Acinetobacter calcoaceticus is a classical quinoprotein. It requires the cofactor pyrroloquinoline quinone (PQQ) to catalyze the oxidation of glucose to gluconolactone. The precise catalytic role of PQQ in s-GDH and several other PQQ-dependent enzymes has remained controversial because of the absence of comprehensive structural data. We have determined the crystal structure of a ternary complex of s-GDH with PQQ and methylhydrazine, a competitive inhibitor of the enzyme. This complex, refined at 1.5-A resolution to an R factor of 16.7%, affords a detailed view of a cofactor-binding site of s-GDH. Moreover, it presents the first direct observation of covalent PQQ adduct in the active-site of a PQQ-dependent enzyme, thereby confirming previous evidence that the C5 carbonyl group of the cofactor is the most reactive moiety of PQQ.
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Affiliation(s)
- A Oubrie
- Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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46
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Casini A, Finazzi-Agrò A, Sabatini S, El-Sherbini ES, Tortorella S, Scipione L. Role of calcium in the reaction between pyrroloquinoline quinone and pyridine nucleotides monomers and dimers. Arch Biochem Biophys 1999; 368:385-93. [PMID: 10441392 DOI: 10.1006/abbi.1999.1270] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Redox reactions were carried out in aerobiosis and anaerobiosis between NAD(P) dimers or NAD(P)H and pyrroloquinoline quinone (PQQ) in different buffers. The buffer system and pH significantly affected the oxidation rates of nucleotides and the ESR signal intensity of the PQQ(*) radical formed in anaerobiosis by comproportion between the quinone and quinol forms. The relative reactivity of the four nucleotides toward PQQ was affected by pH and buffer nature. PQQ, which behaves as an electron shuttle from nucleotides to oxygen, was first converted to PQQH(2) and then rapidly reoxidized by oxygen, with formation of hydrogen peroxide. Both NAD(P) dimers and NAD(P)H consumed 1 mol of oxygen per mole of reacted molecule of pyridine nucleotide, yielding 1 or 2 mol of NAD(P)(+) from NAD(P)H or from NAD(P) dimers, respectively. Chelating agents such as EDTA and phytate strongly decreased the reaction rate and the PQQ(*) radical signal intensity. Kinetics carried out in the presence of metal ions showed instead an increased reaction rate in the order Ca(2+) >> Mg(2+) > Na(+) >> K(+). Spectrofluorimetric measurements of PQQ with increasing concentrations of Ca(2+) showed a fluorescence quenching and shift of the maximum emission toward lower wavelengths, while other metal ions showed minor effects, if any. Therefore, it is demonstrated that Ca(2+) binds to PQQ, probably forming a complex which is more reactive with both one-electron (NAD(P) dimers) or two-electron donors (NAD(P)H) in nonenzymic reactions. It is important to recall that Ca(2+) was already found to play active role in PQQ-containing enzymes.
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Affiliation(s)
- A Casini
- Dipartimento di Studi di Chimica e Tecnologia delle Sostanze Biologicamente Attive, Università "La Sapienza,", Rome, Italy
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Mitchell AE, Jones AD, Mercer RS, Rucker RB. Characterization of pyrroloquinoline quinone amino acid derivatives by electrospray ionization mass spectrometry and detection in human milk. Anal Biochem 1999; 269:317-25. [PMID: 10222004 DOI: 10.1006/abio.1999.4039] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe a HPLC method coupled to electrospray ionization mass spectrometry (ESI/MS) for quantification and identification of pyrroloquinoline quinone (PQQ) and condensation products formed upon incubation of PQQ with amino acids (IPQ; imidazolopyrroloquinoline and I/OPQ/R; imidazolopyrroloquinoline with attached R-group). More importantly, using these methods we demonstrate the presence of both PQQ and IPQ in human milk in nanomolar to micromolar concentrations. PQQ was incubated with amino acids and condensation products were separated by HPLC. Fractions corresponding to each product were collected and molecular masses were determined using ESI/MS. Ala, Asp, Arg, Cys, Gly, Glu, Ser, Thr, Trp, and Tyr form IPQ upon incubation with PQQ. Yields of IPQ were low (<5%) for Asp and Glu, yet high (>60%) for Thr. In addition to IPQ, Ala, Arg, Cys, Ser, Trp, and Tyr formed IPQ/R derivatives. His, Ile, Leu, Glu, Leu, Lys, Met, and Phe form only IPQ/R derivatives. Proline did not react with PQQ. Mass spectra indicate that PQQ forms stable hydrated carbonyls and decarboxylates easily. Although mass spectra were complicated by the oxidation state of the quinone and decarboxylation of PQQ, these methods are invaluable for the rapid detection of the full range of PQQ adducts in biological matrices.
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Affiliation(s)
- A E Mitchell
- Department of Nutrition, University of California, Davis, California 95616-8669, USA
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