1
|
Manickas EC, LaLonde AB, Hu MY, Alp EE, Lehnert N. Stabilization of a Heme-HNO Model Complex Using a Bulky Bis-Picket Fence Porphyrin and Reactivity Studies with NO. J Am Chem Soc 2023; 145:23014-23026. [PMID: 37824502 DOI: 10.1021/jacs.3c05333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Nitroxyl, HNO/NO-, the one-electron reduced form of NO, is suggested to take part in distinct signaling pathways in mammals and is also a key intermediate in various heme-catalyzed NOx interconversions in the nitrogen cycle. Cytochrome P450nor (Cyt P450nor) is a heme-containing enzyme that performs NO reduction to N2O in fungal denitrification. The reactive intermediate in this enzyme, termed "Intermediate I", is proposed to be an Fe-NHO/Fe-NHOH type species, but it is difficult to study its electronic structure and exact protonation state due to its instability. Here, we utilize a bulky bis-picket fence porphyrin to obtain the first stable heme-HNO model complex, [Fe(3,5-Me-BAFP)(MI)(NHO)], as a model for Intermediate I, and more generally HNO adducts of heme proteins. Due to the steric hindrance of the bis-picket fence porphyrin, [Fe(3,5-Me-BAFP)(MI)(NHO)] is stable (τ1/2 = 56 min at -30 °C), can be isolated as a solid, and is available for thorough spectroscopic characterization. In particular, we were able to solve a conundrum in the literature and provide the first full vibrational characterization of a heme-HNO complex using IR and nuclear resonance vibrational spectroscopy (NRVS). Reactivity studies of [Fe(3,5-Me-BAFP)(MI)(NHO)] with NO gas show a 91 ± 10% yield for N2O formation, demonstrating that heme-HNO complexes are catalytically competent intermediates for NO reduction to N2O in Cyt P450nor. The implications of these results for the mechanism of Cyt P450nor are further discussed.
Collapse
Affiliation(s)
- Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, The University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Ashley B LaLonde
- Department of Chemistry and Department of Biophysics, The University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Michael Y Hu
- Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, Illinois 60439, United States
| | - E Ercan Alp
- Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, Illinois 60439, United States
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, The University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| |
Collapse
|
2
|
Takeda H, Shimba K, Horitani M, Kimura T, Nomura T, Kubo M, Shiro Y, Tosha T. Trapping of a Mononitrosyl Nonheme Intermediate of Nitric Oxide Reductase by Cryo-Photolysis of Caged Nitric Oxide. J Phys Chem B 2023; 127:846-854. [PMID: 36602896 DOI: 10.1021/acs.jpcb.2c05852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Characterization of short-lived reaction intermediates is essential for elucidating the mechanism of the reaction catalyzed by metalloenzymes. Here, we demonstrated that the photolysis of a caged compound under cryogenic temperature followed by thermal annealing is an invaluable technique for trapping of short-lived reaction intermediates of metalloenzymes through the study of membrane-integrated nitric oxide reductase (NOR) that catalyzes reductive coupling of two NO molecules to N2O at its heme/nonheme FeB binuclear center. Although NO produced by the photolysis of caged NO did not react with NOR under cryogenic temperature, annealing to ∼160 K allowed NO to diffuse and react with NOR, which was evident from the appearance of EPR signals assignable to the S = 3/2 state. This indicates that the nonheme FeB-NO species can be trapped as the intermediate. Time-resolved IR spectroscopy with the use of the photolysis of caged NO as a reaction trigger showed that the intermediate formed at 10 μs gave the NO stretching frequency at 1683 cm-1 typical of nonheme Fe-NO, confirming that the combination of the cryo-photolysis of caged NO and annealing enabled us to trap the reaction intermediate. Thus, the cryo-photolysis of the caged compound has great potential for the characterization of short-lived reaction intermediates.
Collapse
Affiliation(s)
- Hanae Takeda
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan.,RIKEN SPring-8 center, Sayo, Hyogo 679-5148, Japan
| | - Kanji Shimba
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan.,RIKEN SPring-8 center, Sayo, Hyogo 679-5148, Japan
| | - Masaki Horitani
- Department of Applied Biochemistry & Food Science, Saga University, Saga 840-8502, Japan.,The United Graduate School of Agricultural Science, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Tetsunari Kimura
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Takashi Nomura
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Minoru Kubo
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Takehiko Tosha
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan.,RIKEN SPring-8 center, Sayo, Hyogo 679-5148, Japan
| |
Collapse
|
3
|
Tosha T. Visualization of Enzymatic Reaction by Time-resolved Structural Analysis with Photosensitive Caged Substrate. YAKUGAKU ZASSHI 2022; 142:487-494. [DOI: 10.1248/yakushi.21-00203-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
4
|
Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
Collapse
Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| |
Collapse
|
5
|
Midlik A, Navrátilová V, Moturu TR, Koča J, Svobodová R, Berka K. Uncovering of cytochrome P450 anatomy by SecStrAnnotator. Sci Rep 2021; 11:12345. [PMID: 34117311 PMCID: PMC8196199 DOI: 10.1038/s41598-021-91494-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/21/2021] [Indexed: 12/25/2022] Open
Abstract
Protein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of structures, and the SSEs can help to orient within them. Communities around specific protein families have even developed specialized SSE annotations, always assigning the same name to the equivalent SSEs in homologous proteins. A detailed analysis of the groups of equivalent SSEs provides an overview of the studied family and enriches the analysis of any particular protein at hand. We developed a workflow for the analysis of the secondary structure anatomy of a protein family. We applied this analysis to the model family of cytochromes P450 (CYPs)-a family of important biotransformation enzymes with a community-wide used SSE annotation. We report the occurrence, typical length and amino acid sequence for the equivalent SSE groups, the conservation/variability of these properties and relationship to the substrate recognition sites. We also suggest a generic residue numbering scheme for the CYP family. Comparing the bacterial and eukaryotic part of the family highlights the significant differences and reveals a well-known anomalous group of bacterial CYPs with some typically eukaryotic features. Our workflow for SSE annotation for CYP and other families can be freely used at address https://sestra.ncbr.muni.cz .
Collapse
Affiliation(s)
- Adam Midlik
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Veronika Navrátilová
- Department of Physical Chemistry, Faculty of Science, Palacký University, Olomouc, 771 46, Czech Republic
| | - Taraka Ramji Moturu
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Radka Svobodová
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic.
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic.
| | - Karel Berka
- Department of Physical Chemistry, Faculty of Science, Palacký University, Olomouc, 771 46, Czech Republic.
| |
Collapse
|
6
|
Reed CJ, Lam QN, Mirts EN, Lu Y. Molecular understanding of heteronuclear active sites in heme-copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modelling. Chem Soc Rev 2021; 50:2486-2539. [PMID: 33475096 PMCID: PMC7920998 DOI: 10.1039/d0cs01297a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Heme-copper oxidases (HCO), nitric oxide reductases (NOR), and sulfite reductases (SiR) catalyze the multi-electron and multi-proton reductions of O2, NO, and SO32-, respectively. Each of these reactions is important to drive cellular energy production through respiratory metabolism and HCO, NOR, and SiR evolved to contain heteronuclear active sites containing heme/copper, heme/nonheme iron, and heme-[4Fe-4S] centers, respectively. The complexity of the structures and reactions of these native enzymes, along with their large sizes and/or membrane associations, make it challenging to fully understand the crucial structural features responsible for the catalytic properties of these active sites. In this review, we summarize progress that has been made to better understand these heteronuclear metalloenzymes at the molecular level though study of the native enzymes along with insights gained from biomimetic models comprising either small molecules or proteins. Further understanding the reaction selectivity of these enzymes is discussed through comparisons of their similar heteronuclear active sites, and we offer outlook for further investigations.
Collapse
Affiliation(s)
- Christopher J Reed
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA.
| | - Quan N Lam
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA
| | - Evan N Mirts
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA. and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
7
|
He Z, Deng H, Wang Q, Li Y, Liang X, Liu D, Wu Y. Electrochemical and spectroscopic characteristics of cytochrome P450 55A3 and its interaction with nitric oxide. Int J Biol Macromol 2020; 167:1406-1413. [PMID: 33202279 DOI: 10.1016/j.ijbiomac.2020.11.094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/17/2020] [Accepted: 11/12/2020] [Indexed: 11/30/2022]
Abstract
Cytochrome P450 55A3 (CYP55A3) is an enzyme with the catalytic activity of nitric oxide (NO) to nitrous oxide using NADH or NADPH as the electron donor. Herein CYP55A3 has been expressed in E. coli and purified by His-tag columns. The electrochemical and spectroscopic characteristic of CYP55A3 and its interaction with NO has been studied. The direct electrochemistry of Fe3+/Fe2+ redox peaks in CYP55A3 was realized on the pyrolitic graphite electrode with the redox potential of -475 mV in pH 7.0 phosphate buffer. With the addition of NO a ferric nitroxyl complex (Fe3+-NO) formed with a new reduction peak at -0.78 V. The reduction peak current increased with the concentration of NO and showed typical Michaelis-Menten kinetic characteristics with the apparent Michaelis constant Kmapp 9.78 μM. The binding constant K calculated to be 3.93 × 104 M by UV-vis method. The fluorescence emission spectra of iron porphyrin in CYP55A3 showed with the peak wavelength 633 nm, and its fluorescence intensity increased after binding with NO. The fluorescence analysis demonstrated that NADH can relay electrons to iron porphyrin and reduce NO. The reductive product of NO released and the iron porphyrin in CYP55A3 turned back to the original form.
Collapse
Affiliation(s)
- Zheng He
- College of Life Science, South Central University for Nationalities, Wuhan 430074, PR China
| | - Huan Deng
- College of Life Science, South Central University for Nationalities, Wuhan 430074, PR China
| | - Qiang Wang
- College of Pharmacy, South Central University for Nationalities, Wuhan 430074, PR China
| | - Yong Li
- College of Life Science, South Central University for Nationalities, Wuhan 430074, PR China
| | - Xiaosheng Liang
- College of Life Science, South Central University for Nationalities, Wuhan 430074, PR China
| | - Deli Liu
- College of Life Science, Central China Normal University, Wuhan 430079, PR China
| | - Yunhua Wu
- College of Life Science, South Central University for Nationalities, Wuhan 430074, PR China.
| |
Collapse
|
8
|
Ferousi C, Majer SH, DiMucci IM, Lancaster KM. Biological and Bioinspired Inorganic N-N Bond-Forming Reactions. Chem Rev 2020; 120:5252-5307. [PMID: 32108471 PMCID: PMC7339862 DOI: 10.1021/acs.chemrev.9b00629] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.
Collapse
Affiliation(s)
- Christina Ferousi
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Sean H Majer
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Ida M DiMucci
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| |
Collapse
|
9
|
Shi X, Chuo SW, Liou SH, Goodin DB. Double Electron–Electron Resonance Shows That the Substrate but Not the Inhibitors Causes Disorder in the F/G Loop of CYP119 in Solution. Biochemistry 2020; 59:1823-1831. [DOI: 10.1021/acs.biochem.0c00171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Xiaoxiao Shi
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Shih-Wei Chuo
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Shu-Hao Liou
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - David B. Goodin
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| |
Collapse
|
10
|
Suga M, Shimada A, Akita F, Shen JR, Tosha T, Sugimoto H. Time-resolved studies of metalloproteins using X-ray free electron laser radiation at SACLA. Biochim Biophys Acta Gen Subj 2019; 1864:129466. [PMID: 31678142 DOI: 10.1016/j.bbagen.2019.129466] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/02/2019] [Accepted: 10/04/2019] [Indexed: 01/12/2023]
Abstract
BACKGROUND The invention of the X-ray free-electron laser (XFEL) has provided unprecedented new opportunities for structural biology. The advantage of XFEL is an intense pulse of X-rays and a very short pulse duration (<10 fs) promising a damage-free and time-resolved crystallography approach. SCOPE OF REVIEW Recent time-resolved crystallographic analyses in XFEL facility SACLA are reviewed. Specifically, metalloproteins involved in the essential reactions of bioenergy conversion including photosystem II, cytochrome c oxidase and nitric oxide reductase are described. MAJOR CONCLUSIONS XFEL with pump-probe techniques successfully visualized the process of the reaction and the dynamics of a protein. Since the active center of metalloproteins is very sensitive to the X-ray radiation, damage-free structures obtained by XFEL are essential to draw mechanistic conclusions. Methods and tools for sample delivery and reaction initiation are key for successful measurement of the time-resolved data. GENERAL SIGNIFICANCE XFEL is at the center of approaches to gain insight into complex mechanism of structural dynamics and the reactions catalyzed by biological macromolecules. Further development has been carried out to expand the application of time-resolved X-ray crystallography. This article is part of a Special Issue entitled Novel measurement techniques for visualizing 'live' protein molecules.
Collapse
Affiliation(s)
- Michihiro Suga
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan..
| | - Atsuhiro Shimada
- Graduate School of Applied Biological Sciences and Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan..
| | - Fusamichi Akita
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan
| | - Takehiko Tosha
- Synchrotron Radiation Life Science Instrumentation Team, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hiroshi Sugimoto
- Synchrotron Radiation Life Science Instrumentation Team, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan..
| |
Collapse
|
11
|
Gu M, Wang M, Guo J, Shi C, Deng J, Huang L, Huang L, Chang Z. Crystal structure of CYP76AH1 in 4-PI-bound state from Salvia miltiorrhiza. Biochem Biophys Res Commun 2019; 511:813-819. [DOI: 10.1016/j.bbrc.2019.02.103] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 11/28/2022]
|
12
|
A novel thermophilic hemoprotein scaffold for rational design of biocatalysts. J Biol Inorg Chem 2018; 23:1295-1307. [PMID: 30209579 DOI: 10.1007/s00775-018-1615-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 09/03/2018] [Indexed: 10/28/2022]
Abstract
Hemoproteins are commonly found in nature, and involved in many important cellular processes such as oxygen transport, electron transfer, and catalysis. Rational design of hemoproteins can not only inspire novel biocatalysts but will also lead to a better understanding of structure-function relationships in native hemoproteins. Here, the heme nitric oxide/oxygen-binding protein from Caldanaerobacter subterraneus subsp. tengcongensis (TtH-NOX) is used as a novel scaffold for oxidation biocatalyst design. We show that signaling protein TtH-NOX can be reengineered to catalyze H2O2 decomposition and oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) by H2O2. In addition, the role of the distal tyrosine (Tyr140) in catalysis is investigated. The mutation of Tyr140 to alanine hinders the catalysis of the oxidation reactions. On the other hand, the mutation of Tyr140 to histidine, which is commonly observed in peroxidases, leads to a significant increase of the catalytic activity. Taken together, these results show that, while the distal histidine plays an important role in hemoprotein reactions with H2O2, it is not always essential for oxidation activity. We show that TtH-NOX protein can be used as an alternative scaffold for the design of novel biocatalysts with desired reactivity or functionality. H-NOX proteins are homologous to the nitric oxide sensor soluble guanylate cyclase. Here, we show that the gas sensor protein TtH-NOX shows limited capacity for catalysis of redox reactions and it can be used as a novel scaffold in biocatalysis design.
Collapse
|
13
|
Miyanaga A, Takayanagi R, Furuya T, Kawamata A, Itagaki T, Iwabuchi Y, Kanoh N, Kudo F, Eguchi T. Substrate Recognition by a Dual-Function P450 Monooxygenase GfsF Involved in FD-891 Biosynthesis. Chembiochem 2017; 18:2179-2187. [PMID: 28869713 DOI: 10.1002/cbic.201700429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Indexed: 12/22/2022]
Abstract
GfsF is a multifunctional P450 monooxygenase that catalyzes epoxidation and subsequent hydroxylation in the biosynthesis of macrolide polyketide FD-891. Here, we describe the biochemical and structural analysis of GfsF. To obtain the structural basis of a dual-function reaction, we determined the crystal structure of ligand-free GfsF, which revealed GfsF to have a predominantly hydrophobic substrate binding pocket. The docking models, in conjunction with the results of the enzymatic assay with substrate analogues and site-directed mutagenesis suggested two distinct substrate binding modes for epoxidation and hydroxylation reactions, which explained how GfsF regulates the order of two oxidative reactions. These findings provide new insights into the reaction mechanism of multifunctional P450 monooxygenases.
Collapse
Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Ryuichi Takayanagi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Takashi Furuya
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Ayano Kawamata
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Tomohiro Itagaki
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Yoshiharu Iwabuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Naoki Kanoh
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| |
Collapse
|
14
|
Scheidt WR, Li J, Sage JT. What Can Be Learned from Nuclear Resonance Vibrational Spectroscopy: Vibrational Dynamics and Hemes. Chem Rev 2017; 117:12532-12563. [PMID: 28921972 PMCID: PMC5639469 DOI: 10.1021/acs.chemrev.7b00295] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Nuclear resonance
vibrational spectroscopy (NRVS; also known as
nuclear inelastic scattering, NIS) is a synchrotron-based method that
reveals the full spectrum of vibrational dynamics for Mössbauer
nuclei. Another major advantage, in addition to its completeness (no
arbitrary optical selection rules), is the unique selectivity of NRVS.
The basics of this recently developed technique are first introduced
with descriptions of the experimental requirements and data analysis
including the details of mode assignments. We discuss the use of NRVS
to probe 57Fe at the center of heme and heme protein derivatives
yielding the vibrational density of states for the iron. The application
to derivatives with diatomic ligands (O2, NO, CO, CN–) shows the strong capabilities of identifying mode
character. The availability of the complete vibrational spectrum of
iron allows the identification of modes not available by other techniques.
This permits the correlation of frequency with other physical properties.
A significant example is the correlation we find between the Fe–Im
stretch in six-coordinate Fe(XO) hemes and the trans Fe–N(Im)
bond distance, not possible previously. NRVS also provides uniquely
quantitative insight into the dynamics of the iron. For example, it
provides a model-independent means of characterizing the strength
of iron coordination. Prediction of the temperature-dependent mean-squared
displacement from NRVS measurements yields a vibrational “baseline”
for Fe dynamics that can be compared with results from techniques
that probe longer time scales to yield quantitative insights into
additional dynamical processes.
Collapse
Affiliation(s)
- W Robert Scheidt
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556 United States
| | - Jianfeng Li
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences , YanQi Lake, HuaiRou District, Beijing 101408, China
| | - J Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , 120 Forsyth Street, Boston, Massachusetts 02115, United States
| |
Collapse
|
15
|
Harris KL, Thomson RES, Strohmaier SJ, Gumulya Y, Gillam EMJ. Determinants of thermostability in the cytochrome P450 fold. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:97-115. [PMID: 28822812 DOI: 10.1016/j.bbapap.2017.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/19/2017] [Accepted: 08/07/2017] [Indexed: 10/19/2022]
Abstract
Cytochromes P450 are found throughout the biosphere in a wide range of environments, serving a multitude of physiological functions. The ubiquity of the P450 fold suggests that it has been co-opted by evolution many times, and likely presents a useful compromise between structural stability and conformational flexibility. The diversity of substrates metabolized and reactions catalyzed by P450s makes them attractive starting materials for use as biocatalysts of commercially useful reactions. However, process conditions impose different requirements on enzymes to those in which they have evolved naturally. Most natural environments are relatively mild, and therefore most P450s have not been selected in Nature for the ability to withstand temperatures above ~40°C, yet industrial processes frequently require extended incubations at much higher temperatures. Thus, there has been considerable interest and effort invested in finding or engineering thermostable P450 systems. Numerous P450s have now been identified in thermophilic organisms and analysis of their structures provides information as to mechanisms by which the P450 fold can be stabilized. In addition, protein engineering, particularly by directed or artificial evolution, has revealed mutations that serve to stabilize particular mesophilic enzymes of interest. Here we review the current understanding of thermostability as it applies to the P450 fold, gleaned from the analysis of P450s characterized from thermophilic organisms and the parallel engineering of mesophilic forms for greater thermostability. We then present a perspective on how this information might be used to design stable P450 enzymes for industrial application. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
Collapse
Affiliation(s)
- Kurt L Harris
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Australia
| | - Raine E S Thomson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Australia
| | - Silja J Strohmaier
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Australia
| | - Yosephine Gumulya
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Australia
| | - Elizabeth M J Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Australia.
| |
Collapse
|
16
|
Shakoor A, Abdullah M, Yousaf B, Amina, Ma Y. Atmospheric emission of nitric oxide and processes involved in its biogeochemical transformation in terrestrial environment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016:10.1007/s11356-016-7823-6. [PMID: 27771880 DOI: 10.1007/s11356-016-7823-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 10/03/2016] [Indexed: 06/06/2023]
Abstract
Nitric oxide (NO) is an intra- and intercellular gaseous signaling molecule with a broad spectrum of regulatory functions in biological system. Its emissions are produced by both natural and anthropogenic sources; however, soils are among the most important sources of NO. Nitric oxide plays a decisive role in environmental-atmospheric chemistry by controlling the tropospheric photochemical production of ozone and regulates formation of various oxidizing agents such as hydroxyl radical (OH), which contributes to the formation of acid of precipitates. Consequently, for developing strategies to overcome the deleterious impact of NO on terrestrial ecosystem, it is mandatory to have reliable information about the exact emission mechanism and processes involved in its transformation in soil-atmospheric system. Although the formation process of NO is a complex phenomenon and depends on many physicochemical characteristics, such as organic matter, soil pH, soil moisture, soil temperature, etc., this review provides comprehensive updates about the emission characteristics and biogeochemical transformation mechanism of NO. Moreover, this article will also be helpful to understand the processes involved in the consumption of NO in soils. Further studies describing the functions of NO in biological system are also discussed.
Collapse
Affiliation(s)
- Awais Shakoor
- School of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Muhammad Abdullah
- State-Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Balal Yousaf
- CAS-Key Laboratory of Crust-Mantle Materials and the Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Amina
- School of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Youhua Ma
- School of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China.
| |
Collapse
|
17
|
Romão CV, Vicente JB, Borges PT, Frazão C, Teixeira M. The dual function of flavodiiron proteins: oxygen and/or nitric oxide reductases. J Biol Inorg Chem 2016; 21:39-52. [PMID: 26767750 DOI: 10.1007/s00775-015-1329-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/28/2015] [Indexed: 12/27/2022]
Abstract
Flavodiiron proteins have emerged in the last two decades as a newly discovered family of oxygen and/or nitric oxide reductases widespread in the three life domains, and present in both aerobic and anaerobic organisms. Herein we present the main features of these fascinating enzymes, with a particular emphasis on the metal sites, as more appropriate for this special issue in memory of the exceptional bioinorganic scientist R. J. P. Williams who pioneered the notion of (metal) element availability-driven evolution. We also compare the flavodiiron proteins with the other oxygen and nitric oxide reductases known until now, highlighting how throughout evolution Nature arrived at different solutions for similar functions, in some cases adding extra features, such as energy conservation. These enzymes are an example of the (bioinorganic) unpredictable diversity of the living world.
Collapse
Affiliation(s)
- Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - João B Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal.
| |
Collapse
|
18
|
Sakaguchi M, Kimura T, Nishida T, Tosha T, Sugimoto H, Yamaguchi Y, Yanagisawa S, Ueno G, Murakami H, Ago H, Yamamoto M, Ogura T, Shiro Y, Kubo M. A nearly on-axis spectroscopic system for simultaneously measuring UV-visible absorption and X-ray diffraction in the SPring-8 structural genomics beamline. JOURNAL OF SYNCHROTRON RADIATION 2016; 23:334-8. [PMID: 26698082 PMCID: PMC5356500 DOI: 10.1107/s1600577515018275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 09/29/2015] [Indexed: 05/23/2023]
Abstract
UV-visible absorption spectroscopy is useful for probing the electronic and structural changes of protein active sites, and thus the on-line combination of X-ray diffraction and spectroscopic analysis is increasingly being applied. Herein, a novel absorption spectrometer was developed at SPring-8 BL26B2 with a nearly on-axis geometry between the X-ray and optical axes. A small prism mirror was placed near the X-ray beamstop to pass the light only 2° off the X-ray beam, enabling spectroscopic analysis of the X-ray-exposed volume of a crystal during X-ray diffraction data collection. The spectrometer was applied to NO reductase, a heme enzyme that catalyzes NO reduction to N2O. Radiation damage to the heme was monitored in real time during X-ray irradiation by evaluating the absorption spectral changes. Moreover, NO binding to the heme was probed via caged NO photolysis with UV light, demonstrating the extended capability of the spectrometer for intermediate analysis.
Collapse
Affiliation(s)
- Miyuki Sakaguchi
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Akoh, Hyogo 678-1297, Japan
| | | | - Takuma Nishida
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Akoh, Hyogo 678-1297, Japan
| | - Takehiko Tosha
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | | | - Yoshihiro Yamaguchi
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Akoh, Hyogo 678-1297, Japan
| | - Sachiko Yanagisawa
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Akoh, Hyogo 678-1297, Japan
| | - Go Ueno
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | | | - Hideo Ago
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Masaki Yamamoto
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Takashi Ogura
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Akoh, Hyogo 678-1297, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Akoh, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Minoru Kubo
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| |
Collapse
|
19
|
Lehnert N, Peters JC. Preface for Small-Molecule Activation: From Biological Principles to Energy Applications. Part 2: Small Molecules Related to the Global Nitrogen Cycle. Inorg Chem 2015; 54:9229-33. [DOI: 10.1021/acs.inorgchem.5b02124] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry, The University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
| | - Jonas C. Peters
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| |
Collapse
|
20
|
Yang Y, Zhang H, Usharani D, Bu W, Im S, Tarasev M, Rwere F, Pearl NM, Meagher J, Sun C, Stuckey J, Shaik S, Waskell L. Structural and functional characterization of a cytochrome P450 2B4 F429H mutant with an axial thiolate-histidine hydrogen bond. Biochemistry 2014; 53:5080-91. [PMID: 25029089 PMCID: PMC4131899 DOI: 10.1021/bi5003794] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 07/15/2014] [Indexed: 02/02/2023]
Abstract
The structural basis of the regulation of microsomal cytochrome P450 (P450) activity was investigated by mutating the highly conserved heme binding motif residue, Phe429, on the proximal side of cytochrome P450 2B4 to a histidine. Spectroscopic, pre-steady-state and steady-state kinetic, thermodynamic, theoretical, and structural studies of the mutant demonstrate that formation of an H-bond between His429 and the unbonded electron pair of the Cys436 axial thiolate significantly alters the properties of the enzyme. The mutant lost >90% of its activity; its redox potential was increased by 87 mV, and the half-life of the oxyferrous mutant was increased ∼37-fold. Single-crystal electronic absorption and resonance Raman spectroscopy demonstrated that the mutant was reduced by a small dose of X-ray photons. The structure revealed that the δN atom of His429 forms an H-bond with the axial Cys436 thiolate whereas the εN atom forms an H-bond with the solvent and the side chain of Gln357. The amide of Gly438 forms the only other H-bond to the tetrahedral thiolate. Theoretical quantification of the histidine-thiolate interaction demonstrates a significant electron withdrawing effect on the heme iron. Comparisons of structures of class I-IV P450s demonstrate that either a phenylalanine or tryptophan is often found at the location corresponding to Phe429. Depending on the structure of the distal pocket heme, the residue at this location may or may not regulate the thermodynamic properties of the P450. Regardless, this residue appears to protect the thiolate from solvent, oxidation, protonations, and other deleterious reactions.
Collapse
Affiliation(s)
- Yuting Yang
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Haoming Zhang
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Dandamudi Usharani
- Institute
of Chemistry and Lise Meitner-Minerva Center for Computational Quantum
Chemistry, Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Weishu Bu
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Sangchoul Im
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Michael Tarasev
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Freeborn Rwere
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Naw May Pearl
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Jennifer Meagher
- Life
Science Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Cuthbert Sun
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Jeanne Stuckey
- Life
Science Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Sason Shaik
- Institute
of Chemistry and Lise Meitner-Minerva Center for Computational Quantum
Chemistry, Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Lucy Waskell
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| |
Collapse
|
21
|
A Eukaryotic Copper-Containing Nitrite Reductase Derived from a NirK Homolog Gene ofAspergillus oryzae. Biosci Biotechnol Biochem 2014; 74:984-91. [DOI: 10.1271/bbb.90844] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
22
|
Riplinger C, Bill E, Daiber A, Ullrich V, Shoun H, Neese F. New Insights into the Nature of Observable Reaction Intermediates in Cytochrome P450 NO Reductase by Using a Combination of Spectroscopy and Quantum Mechanics/Molecular Mechanics Calculations. Chemistry 2014; 20:1602-14. [DOI: 10.1002/chem.201302443] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 11/04/2013] [Indexed: 11/08/2022]
|
23
|
Goodrich LE, Roy S, Alp EE, Zhao J, Hu MY, Lehnert N. Electronic Structure and Biologically Relevant Reactivity of Low-Spin {FeNO}8 Porphyrin Model Complexes: New Insight from a Bis-Picket Fence Porphyrin. Inorg Chem 2013; 52:7766-80. [DOI: 10.1021/ic400977h] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lauren E. Goodrich
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109,
United States
| | - Saikat Roy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109,
United States
| | - E. Ercan Alp
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439,
United States
| | - Jiyong Zhao
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439,
United States
| | - Michael Y. Hu
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439,
United States
| | - Nicolai Lehnert
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109,
United States
| |
Collapse
|
24
|
Shiro Y, Sugimoto H, Tosha T, Nagano S, Hino T. Structural basis for nitrous oxide generation by bacterial nitric oxide reductases. Philos Trans R Soc Lond B Biol Sci 2012; 367:1195-203. [PMID: 22451105 DOI: 10.1098/rstb.2011.0310] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The crystal structure of the bacterial nitric oxide reductase (cNOR) from Pseudomonas aeruginosa is reported. Its overall structure is similar to those of the main subunit of aerobic and micro-aerobic cytochrome oxidases (COXs), in agreement with the hypothesis that all these enzymes are members of the haem-copper oxidase superfamily. However, substantial structural differences between cNOR and COX are observed in the catalytic centre and the delivery pathway of the catalytic protons, which should be reflected in functional differences between these respiratory enzymes. On the basis of the cNOR structure, we propose a possible reaction mechanism of nitric oxide reduction to nitrous oxide as a working hypothesis.
Collapse
|
25
|
Shoun H, Fushinobu S, Jiang L, Kim SW, Wakagi T. Fungal denitrification and nitric oxide reductase cytochrome P450nor. Philos Trans R Soc Lond B Biol Sci 2012; 367:1186-94. [PMID: 22451104 DOI: 10.1098/rstb.2011.0335] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have shown that many fungi (eukaryotes) exhibit distinct denitrifying activities, although occurrence of denitrification was previously thought to be restricted to bacteria (prokaryotes), and have characterized the fungal denitrification system. It comprises NirK (copper-containing nitrite reductase) and P450nor (a cytochrome P450 nitric oxide (NO) reductase (Nor)) to reduce nitrite to nitrous oxide (N(2)O). The system is localized in mitochondria functioning during anaerobic respiration. Some fungal systems further contain and use dissimilatory and assimilatory nitrate reductases to denitrify nitrate. Phylogenetic analysis of nirK genes showed that the fungal-denitrifying system has the same ancestor as the bacterial counterpart and suggested a possibility of its proto-mitochondrial origin. By contrast, fungi that have acquired a P450 from bacteria by horizontal transfer of the gene, modulated its function to give a Nor activity replacing the original Nor with P450nor. P450nor receives electrons directly from nicotinamide adenine dinucleotide to reduce NO to N(2)O. The mechanism of this unprecedented electron transfer has been extensively studied and thoroughly elucidated. Fungal denitrification is often accompanied by a unique phenomenon, co-denitrification, in which a hybrid N(2) or N(2)O species is formed upon the combination of nitrogen atoms of nitrite with a nitrogen donor (amines and imines). Possible involvement of NirK and P450nor is suggested.
Collapse
Affiliation(s)
- Hirofumi Shoun
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
| | | | | | | | | |
Collapse
|
26
|
Krámos B, Menyhárd DK, Oláh J. Direct hydride shift mechanism and stereoselectivity of P450nor confirmed by QM/MM calculations. J Phys Chem B 2012; 116:872-85. [PMID: 22148861 DOI: 10.1021/jp2080918] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Nitric oxide reductase (P450(nor)) found in Fusarium oxysporum catalyzes the reduction of nitric oxide to N(2)O in a multistep process. The reducing agent, NADH, is bound in the distal pocket of the enzyme, and direct hydride transfer occurs from NADH to the nitric oxide bound heme enzyme, forming intermediate I. Here we studied the possibility of hydride transfer from NADH to both the nitrogen and oxygen of the heme-bound nitric oxide, using quantum chemical and combined quantum mechanics/molecular mechanics (QM/MM) calculations, on two different protein models, representing both possible stereochemistries, a syn- and an anti-NADH arrangement. All calculations clearly favor hydride transfer to the nitrogen of nitric oxide, and the QM-only barrier and kinetic isotope effects are good agreement with the experimental values of intermediate I formation. We obtained higher barriers in the QM/MM calculations for both pathways, but hydride transfer to the nitrogen of nitric oxide is still clearly favored. The barriers obtained for the syn, Pro-R conformation of NADH are lower and show significantly less variation than the barriers obtained in the case of anti conformation. The effect of basis set and wide range of functionals on the obtained results are also discussed.
Collapse
Affiliation(s)
- Balázs Krámos
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
| | | | | |
Collapse
|
27
|
Riplinger C, Neese F. The reaction mechanism of Cytochrome P450 NO reductase: a detailed quantum mechanics/molecular mechanics study. Chemphyschem 2011; 12:3192-203. [PMID: 22095732 DOI: 10.1002/cphc.201100523] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 10/10/2011] [Indexed: 11/09/2022]
Abstract
A detailed QM/MM study on the reaction mechanism of Cytochrome P450 NO reductase is reported. Two reaction pathways connecting the two well-characterized intermediates as well as two putative intermediates that represent the unknown third intermediate are explored, with emphasis on the unusual direct reduction of the enzymatic active site by the cofactor NADH. Activation barriers and kinetic isotope effect are calculated and reveal that reduction of the NO-bound species occurs in form of a hydride ion transfer. Furthermore, the impact of different hydrogen bonds in the active site to binding and reactivity of NADH is explored. The calculated kinetic and thermodynamic properties for both modelled pathways are used for the kinetic simulation of the entire reaction course. It is thus shown that the unknown key intermediate is the singlet diradical Fe(III)-NHOH(⋅). It is also found that the mechanism of the N-N bond formation is spin-recoupling, which is only possible due to the diradical character of the key intermediate.
Collapse
Affiliation(s)
- Christoph Riplinger
- MPI for Bioinorganic Chemistry, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | | |
Collapse
|
28
|
Hino T, Nagano S, Sugimoto H, Tosha T, Shiro Y. Molecular structure and function of bacterial nitric oxide reductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:680-7. [PMID: 22001779 DOI: 10.1016/j.bbabio.2011.09.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 09/29/2011] [Accepted: 09/29/2011] [Indexed: 10/17/2022]
Abstract
The crystal structure of the membrane-integrated nitric oxide reductase cNOR from Pseudomonas aeruginosa was determined. The smaller NorC subunit of cNOR is comprised of 1 trans-membrane helix and a hydrophilic domain, where the heme c is located, while the larger NorB subunit consists of 12 trans-membrane helices, which contain heme b and the catalytically active binuclear center (heme b(3) and non-heme Fe(B)). The roles of the 5 well-conserved glutamates in NOR are discussed, based on the recently solved structure. Glu211 and Glu280 appear to play an important role in the catalytic reduction of NO at the binuclear center by functioning as a terminal proton donor, while Glu215 probably contributes to the electro-negative environment of the catalytic center. Glu135, a ligand for Ca(2+) sandwiched between two heme propionates from heme b and b(3), and the nearby Glu138 appears to function as a structural factor in maintaining a protein conformation that is suitable for electron-coupled proton transfer from the periplasmic region to the active site. On the basis of these observations, the possible molecular mechanism for the reduction of NO by cNOR is discussed. This article is part of a Special Issue entitled: Respiratory Oxidases.
Collapse
|
29
|
Li Z, Rupasinghe SG, Schuler MA, Nair SK. Crystal structure of a phenol-coupling P450 monooxygenase involved in teicoplanin biosynthesis. Proteins 2011; 79:1728-38. [PMID: 21445994 PMCID: PMC3103887 DOI: 10.1002/prot.22996] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 12/20/2010] [Accepted: 12/27/2010] [Indexed: 11/06/2022]
Abstract
The lipoglycopeptide antibiotic teicoplanin has proven efficacy against gram-positive pathogens. Teicoplanin is distinguished from the vancomycin-type glycopeptide antibiotics, by the presence of an additional cross-link between the aromatic amino acids 1 and 3 that is catalyzed by the cytochrome P450 monooxygenase Orf6* (CYP165D3). As a goal towards understanding the mechanism of this phenol-coupling reaction, we have characterized recombinant Orf6* and determined its crystal structure to 2.2-Å resolution. Although the structure of Orf6* reveals the core fold common to other P450 monooxygenases, there are subtle differences in the disposition of secondary structure elements near the active site cavity necessary to accommodate its complex heptapeptide substrate. Specifically, the orientation of the F and G helices in Orf6* results in a more closed active site than found in the vancomycin oxidative enzymes OxyB and OxyC. In addition, Met226 in the I helix replaces the more typical Gly/Ala residue that is positioned above the heme porphyrin ring, where it forms a hydrogen bond with a heme iron-bound water molecule. Sequence comparisons with other phenol-coupling P450 monooxygenases suggest that Met226 plays a role in determining the substrate regiospecificity of Orf6*. These features provide further insights into the mechanism of the cross-linking mechanisms that occur during glycopeptide antibiotics biosynthesis.
Collapse
Affiliation(s)
- Zhi Li
- Department of Biochemistry, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Sanjeewa G. Rupasinghe
- Department of Cell and Developmental Biology, 1201 W. Gregory Dr., 161 Edward R. Madigan Laboratory, Urbana, IL 61801, USA
- Department of Plant Biology, 1201 W. Gregory Dr., 161 Edward R. Madigan Laboratory, Urbana, IL 61801, USA
| | - Mary A. Schuler
- Department of Biochemistry, 600 S. Mathews Avenue, Urbana, IL 61801, USA
- Department of Cell and Developmental Biology, 1201 W. Gregory Dr., 161 Edward R. Madigan Laboratory, Urbana, IL 61801, USA
- Department of Plant Biology, 1201 W. Gregory Dr., 161 Edward R. Madigan Laboratory, Urbana, IL 61801, USA
| | - Satish K. Nair
- Department of Biochemistry, 600 S. Mathews Avenue, Urbana, IL 61801, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign
| |
Collapse
|
30
|
Pochapsky TC, Kazanis S, Dang M. Conformational plasticity and structure/function relationships in cytochromes P450. Antioxid Redox Signal 2010; 13:1273-96. [PMID: 20446763 PMCID: PMC2959183 DOI: 10.1089/ars.2010.3109] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The cytochrome P450s are a superfamily of enzymes that are found in all kingdoms of living organisms, and typically catalyze the oxidative addition of atomic oxygen to an unactivated C-C or C-H bond. Over 8000 nonredundant sequences of putative and confirmed P450 enzymes have been identified, but three-dimensional structures have been determined for only a small fraction of these. While all P450 enzymes for which structures have been determined share a common global fold, the flexibility and modularity of structure around the active site account for the ability of P450 enzymes to accommodate a vast number of structurally dissimilar substrates and support a wide range of selective oxidations. In this review, known P450 structures are compared, and some structural criteria for prediction of substrate selectivity and reaction type are suggested. The importance of dynamic processes such as redox-dependent and effector-induced conformational changes in determining catalytic competence and regio- and stereoselectivity is discussed, and noncrystallographic methods for characterizing P450 structures and dynamics, in particular, mass spectrometry and nuclear magnetic resonance spectroscopy are reviewed.
Collapse
Affiliation(s)
- Thomas C Pochapsky
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, USA.
| | | | | |
Collapse
|
31
|
Goodrich LE, Paulat F, Praneeth VKK, Lehnert N. Electronic Structure of Heme-Nitrosyls and Its Significance for Nitric Oxide Reactivity, Sensing, Transport, and Toxicity in Biological Systems. Inorg Chem 2010; 49:6293-316. [DOI: 10.1021/ic902304a] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Lauren E. Goodrich
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Florian Paulat
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - V. K. K. Praneeth
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Nicolai Lehnert
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| |
Collapse
|
32
|
Affiliation(s)
- Victor Rosca
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | | | | | | |
Collapse
|
33
|
Crystal structures of cytochrome P450 105P1 from Streptomyces avermitilis: conformational flexibility and histidine ligation state. J Bacteriol 2008; 191:1211-9. [PMID: 19074393 DOI: 10.1128/jb.01276-08] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The polyene macrolide antibiotic filipin is widely used as a probe for cholesterol in biological membranes. The filipin biosynthetic pathway of Streptomyces avermitilis contains two position-specific hydroxylases, C26-specific CYP105P1 and C1'-specific CYP105D6. In this study, we describe the three X-ray crystal structures of CYP105P1: the ligand-free wild-type (WT-free), 4-phenylimidazole-bound wild-type (WT-4PI), and ligand-free H72A mutant (H72A-free) forms. The BC loop region in the WT-free structure has a unique feature; the side chain of His72 within this region is ligated to the heme iron. On the other hand, this region is highly disordered and widely open in WT-4PI and H72A-free structures, respectively. Histidine ligation of wild-type CYP105P1 was not detectable in solution, and a type II spectral change was clearly observed when 4-phenylimidazole was titrated. The H72A mutant showed spectroscopic characteristics that were almost identical to those of the wild-type protein. In the H72A-free structure, there is a large pocket that is of the same size as the filipin molecule. The highly flexible feature of the BC loop region of CYP105P1 may be required to accept a large hydrophobic substrate.
Collapse
|
34
|
Praneeth VKK, Paulat F, Berto TC, George SD, Näther C, Sulok CD, Lehnert N. Electronic Structure of Six-Coordinate Iron(III)−Porphyrin NO Adducts: The Elusive Iron(III)−NO(radical) State and Its Influence on the Properties of These Complexes. J Am Chem Soc 2008; 130:15288-303. [PMID: 18942830 DOI: 10.1021/ja801860u] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- V. K. K. Praneeth
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
| | - Florian Paulat
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
| | - Timothy C. Berto
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
| | - Serena DeBeer George
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
| | - Christian Näther
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
| | - Corinne D. Sulok
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
| | - Nicolai Lehnert
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
| |
Collapse
|
35
|
Modes of heme binding and substrate access for cytochrome P450 CYP74A revealed by crystal structures of allene oxide synthase. Proc Natl Acad Sci U S A 2008; 105:13883-8. [PMID: 18787124 DOI: 10.1073/pnas.0804099105] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cytochrome P450s exist ubiquitously in all organisms and are involved in many biological processes. Allene oxide synthase (AOS) is a P450 enzyme that plays a key role in the biosynthesis of oxylipin jasmonates, which are involved in signal and defense reactions in higher plants. The crystal structures of guayule (Parthenium argentatum) AOS (CYP74A2) and its complex with the substrate analog 13(S)-hydroxyoctadeca-9Z,11E-dienoic acid have been determined. The structures exhibit a classic P450 fold but possess a heme-binding mode with an unusually long heme binding loop and a unique I-helix. The structures also reveal two channels through which substrate and product may access and leave the active site. The entrances are defined by a loop between beta3-2 and beta3-3. Asn-276 in the substrate binding site may interact with the substrate's hydroperoxy group and play an important role in catalysis, and Lys-282 at the entrance may control substrate access and binding. These studies provide both structural insights into AOS and related P450s and a structural basis to understand the distinct reaction mechanism.
Collapse
|
36
|
Chao LY, Rine J, Marletta MA. Spectroscopic and kinetic studies of Nor1, a cytochrome P450 nitric oxide reductase from the fungal pathogen Histoplasma capsulatum. Arch Biochem Biophys 2008; 480:132-7. [PMID: 18804446 DOI: 10.1016/j.abb.2008.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2008] [Revised: 09/05/2008] [Accepted: 09/05/2008] [Indexed: 10/21/2022]
Abstract
The fungal respiratory pathogen Histoplasma capsulatum evades the innate immune response and colonizes macrophages during infection. Although macrophage production of the antimicrobial effector nitric oxide (NO) restricts H. capsulatum growth, the pathogen is able to establish a persistent infection. H. capsulatum contains a P450 nitric oxide reductase homologue (NOR1) that may be important for detoxifying NO during infection. To characterize the activity of this putative P450 enzyme, a 404 amino acid fragment of Nor1p was expressed in Escherichia coli and purified to homogeneity. Spectral characterization of Nor1p indicated that it was similar to other fungal P450 nitric oxide reductases. Nor1p catalyzed the reduction of NO to N2O using NADH as the direct reductant. The K(M) for NO was determined to be 20 microM and the k(cat) to be 5000 min(-1). Together, these results provide evidence for a protective role of a P450 nitric oxide reductase against macrophage-derived NO.
Collapse
Affiliation(s)
- Lily Y Chao
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | | | | |
Collapse
|
37
|
M.A. Abdel B, E.H. Adam S, Takahashi M, Sakamoto A, Shoun H, Morikawa H. A Fungal Cytochrome P-450nor Confers Denitrifying Ability to Tobacco By-2 Cells. ACTA ACUST UNITED AC 2008. [DOI: 10.3923/biotech.2008.250.257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
38
|
Sugimoto H, Shinkyo R, Hayashi K, Yoneda S, Yamada M, Kamakura M, Ikushiro SI, Shiro Y, Sakaki T. Crystal structure of CYP105A1 (P450SU-1) in complex with 1alpha,25-dihydroxyvitamin D3. Biochemistry 2008; 47:4017-27. [PMID: 18314962 DOI: 10.1021/bi7023767] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Vitamin D 3 (VD 3), a prohormone in mammals, plays a crucial role in the maintenance of calcium and phosphorus concentrations in serum. Activation of VD 3 requires 25-hydroxylation in the liver and 1alpha-hydroxylation in the kidney by cytochrome P450 (CYP) enzymes. Bacterial CYP105A1 converts VD 3 into 1alpha,25-dihydroxyvitamin D 3 (1alpha,25(OH) 2D 3) in two independent reactions, despite its low sequence identity with mammalian enzymes (<21% identity). The present study determined the crystal structures of a highly active mutant (R84A) of CYP105A1 from Streptomyces griseolus in complex and not in complex with 1alpha,25(OH) 2D 3. The compound 1alpha,25(OH) 2D 3 is positioned 11 A from the iron atom along the I helix within the pocket. A similar binding mode is observed in the structure of the human CYP2R1-VD 3 complex, indicating a common substrate-binding mechanism for 25-hydroxylation. A comparison with the structure of wild-type CYP105A1 suggests that the loss of two hydrogen bonds in the R84A mutant increases the adaptability of the B' and F helices, creating a transient binding site. Further mutational analysis of the active site reveals that 25- and 1alpha-hydroxylations share residues that participate in these reactions. These results provide the structural basis for understanding the mechanism of the two-step hydroxylation that activates VD 3.
Collapse
Affiliation(s)
- Hiroshi Sugimoto
- RIKEN SPring-8 Center, Harima Institute, Sayo, Hyogo 679-5148, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Yasutake Y, Imoto N, Fujii Y, Fujii T, Arisawa A, Tamura T. Crystal structure of cytochrome P450 MoxA from Nonomuraea recticatena (CYP105). Biochem Biophys Res Commun 2007; 361:876-82. [PMID: 17679139 DOI: 10.1016/j.bbrc.2007.07.062] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Accepted: 07/12/2007] [Indexed: 10/23/2022]
Abstract
Cytochrome P450 MoxA (P450moxA) from a rare actinomycete Nonomuraea recticatena belongs to the CYP105 family and exhibits remarkably broad substrate specificity. Here, we demonstrate that P450moxA acts on several luciferin derivatives, which were originally identified as substrates of the human microsomal P450s. We also describe the crystal structure of P450moxA in substrate-free form. Structural comparison with various bacterial and human microsomal P450s reveals that the P450moxA structure is most closely related to that of the fungal nitric oxide reductase P450nor (CYP55A1). Final refined model of P450moxA comprises almost all the residues, including the "BC-loop" and "FG-loop" regions pivotal for substrate recognition, and the current structure thus defines a well-ordered substrate-binding pocket. Clear electron density map reveals that the MES molecule is bound to the substrate-binding site, and the sixth coordination position of the heme iron is not occupied by a water molecule, probably due to the presence of MES molecule in the vicinity of the heme. The unexpected binding of the MES molecule might reflect the ability of P450moxA to accommodate a broad range of structurally diverse compounds.
Collapse
Affiliation(s)
- Yoshiaki Yasutake
- Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology, 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | | | | | | | | | | |
Collapse
|
40
|
de Groot MT, Merkx M, Koper MT. Bioinspired electrocatalytic reduction of nitric oxide by immobilized heme groups. CR CHIM 2007. [DOI: 10.1016/j.crci.2006.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
41
|
Munro AW, Girvan HM, McLean KJ. Variations on a (t)heme—novel mechanisms, redox partners and catalytic functions in the cytochrome P450 superfamily. Nat Prod Rep 2007; 24:585-609. [PMID: 17534532 DOI: 10.1039/b604190f] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Andrew W Munro
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | | | | |
Collapse
|
42
|
Chiang CW, Yeh HC, Wang LH, Chan NL. Crystal structure of the human prostacyclin synthase. J Mol Biol 2006; 364:266-74. [PMID: 17020766 PMCID: PMC1995163 DOI: 10.1016/j.jmb.2006.09.039] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Revised: 09/13/2006] [Accepted: 09/14/2006] [Indexed: 11/25/2022]
Abstract
Prostacyclin synthase (PGIS) catalyzes an isomerization of prostaglandin H(2) to prostacyclin, a potent mediator of vasodilation and anti-platelet aggregation. Here, we report the crystal structure of human PGIS at 2.15 A resolution, which represents the first three-dimensional structure of a class III cytochrome P450. While notable sequence divergence has been recognized between PGIS and other P450s, PGIS exhibits the typical triangular prism-shaped P450 fold with only moderate structural differences. The conserved acid-alcohol pair in the I helix of P450s is replaced by residues G286 and N287 in PGIS, but the distinctive disruption of the I helix and the presence of a nearby water channel remain conserved. The side-chain of N287 appears to be positioned to facilitate the endoperoxide bond cleavage, suggesting a functional conservation of this residue in O-O bond cleavage. A combination of bent I helix and tilted B' helix creates a channel extending from the heme distal pocket, which seemingly allows binding of various ligands; however, residue W282, placed in this channel at a distance of 8.4 A from the iron with its indole side-chain lying parallel with the porphyrin plane, may serve as a threshold to exclude most ligands from binding. Additionally, a long "meander" region protruding from the protein surface may impede electron transfer. Although the primary sequence of the PGIS cysteine ligand loop diverges significantly from the consensus, conserved tertiary structure and hydrogen bonding pattern are observed for this region. The substrate-binding model was constructed and the structural basis for prostacyclin biosynthesis is discussed.
Collapse
Affiliation(s)
- Chia-Wang Chiang
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung City 402, Taiwan
| | | | | | | |
Collapse
|
43
|
Lehnert N, Praneeth VKK, Paulat F. Electronic structure of iron(II)-porphyrin nitroxyl complexes: Molecular mechanism of fungal nitric oxide reductase (P450nor). J Comput Chem 2006; 27:1338-51. [PMID: 16788909 DOI: 10.1002/jcc.20400] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Density functional calculations are employed to investigate key intermediates of the catalytic cycle of fungal nitric oxide reductase (P450nor). The formal Fe(II)-nitroxyl species Fe(II)--NO/(-) can principally exist in the two spin-states S = 0 and S = 1. In the S = 0 case, a very covalent Fe--NO sigma bond is present, which leads to an electronic structure description that is actually intermediate between Fe(I)--NO and Fe(II)--NO(-). In contrast, the S = 1 case shows a ferrous Fe(II)--NO complex with the extra electron being stored in the pi system of the porphyrin ligand. Importantly, the Fe(II)--NO/(-) species are very basic. The electronic structures and spectroscopic properties of the corresponding N- and O-protonated forms are very different, and unequivocally show that the Mb-HNO adduct (Mb-Myoglobin) prepared by farmer and coworkers is in fact N-protonated. The presence of an axial thiolate ligand enables a second protonation leading to the corresponding Fe(IV)--NHOH- species, which is identified with the catalytically active intermediate I of P450nor. This species reacts with a second molecule of NO by initial electron transfer from NO to Fe(IV) followed by addition of NO+ forming an N--N bond. This is accompanied by an energetically very favorable intramolecular proton transfer leading to the generation of a quite stable Fe(III)--N(OH)(NOH) complex. This way, the enzyme is able to produce dimerized HNO under very controlled conditions and to prevent loss of this ligand from Fe(III). The energetically disfavoured tautomer Fe(III)--N(OH2)(NO) is the catalytically productive species that spontaneously cleaves the N--OH2 bond forming N2O and H2O in a highly exergonic reaction.
Collapse
Affiliation(s)
- Nicolai Lehnert
- Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany.
| | | | | |
Collapse
|
44
|
de Groot MJ. Designing better drugs: predicting cytochrome P450 metabolism. Drug Discov Today 2006; 11:601-6. [PMID: 16793528 DOI: 10.1016/j.drudis.2006.05.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Revised: 04/21/2006] [Accepted: 05/10/2006] [Indexed: 10/24/2022]
Abstract
Many 3D ligand-based and structure-based computational approaches have been used to predict, and thus help explain, the metabolism catalyzed by the enzymes of the cytochrome P450 superfamily (P450s). P450s are responsible for >90% of the metabolism of all drugs, so the computational prediction of metabolism can help to design out drug-drug interactions in the early phases of the drug discovery process. Computational methodologies have focused on a few P450s that are directly involved in drug metabolism. The recently derived crystal structures for human P450s enable better 3D modelling of these important metabolizing enzymes. Models derived for P450s have evolved from simple comparisons of known substrates to more-elaborate experiments that require considerable computer power involving 3D overlaps and docking experiments. These models help to explain and, more importantly, predict the involvement of P450s in the metabolism of specific compounds and guide the drug-design process.
Collapse
Affiliation(s)
- Marcel J de Groot
- Sandwich Chemistry, Pfizer Global Research & Development, Sandwich Laboratories, Kent CT13 9NJ, UK.
| |
Collapse
|
45
|
Menyhárd DK, Keseru GM. Binding mode analysis of the NADH cofactor in nitric oxide reductase: a theoretical study. J Mol Graph Model 2006; 25:363-72. [PMID: 16542862 DOI: 10.1016/j.jmgm.2006.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2004] [Revised: 10/10/2005] [Accepted: 02/13/2006] [Indexed: 11/24/2022]
Abstract
Nitric oxide reductase (Nor), a member of the cytochrome P450 superfamily, takes part in the denitrification process of fungi by reducing NO to N(2)O. Evidence indicates that Nor binds NADH, source of the reducing equivalents of the reaction, within its large hydrophilic ligand binding cavity on the distal side of heme and receives electrons directly from the cofactor. Here we present a binding mode analysis of the structure of the Nor-NO-NADH complex, performed in three steps. The NADH cofactor was first docked into the enzyme interior using the Monte Carlo multiple minimum algorithm, refined by low-mode conformational search and the final arrangement was obtained in a 5ns NPT molecular dynamics simulation. The NADH cofactor, in our results, is positioned--by Arg174, Lys291, Asp393 and several water molecules--within reactive distance of the NO binding spot suggesting a direct hydride shift mechanism between the two. The catalytically required water molecule is captured by NADH and the cofactor not only retains the suggested H-bonded proton transfer pathway between the active site and the solvent, but provides structural restraint for its members. We also found that direct interaction is formed between the cofactor and propionate A of the heme group, which flips from the proximal to the distal side of the heme plane in order to become an H-bonding partner of NADH. The role of Arg64 and Glu71 was suggested to be fixing the residues of the translocated helix B' to their new position.
Collapse
Affiliation(s)
- Dóra K Menyhárd
- Department of Chemical Information Technology, Budapest University of Technology and Economics, Gellért Tér 4., H-1111 Budapest, Hungary.
| | | |
Collapse
|
46
|
Keizers PHJ, Schraven LHM, de Graaf C, Hidestrand M, Ingelman-Sundberg M, van Dijk BR, Vermeulen NPE, Commandeur JNM. Role of the conserved threonine 309 in mechanism of oxidation by cytochrome P450 2D6. Biochem Biophys Res Commun 2005; 338:1065-74. [PMID: 16269134 DOI: 10.1016/j.bbrc.2005.10.066] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2005] [Accepted: 10/09/2005] [Indexed: 11/18/2022]
Abstract
Based on sequence alignments and homology modeling, threonine 309 in cytochrome P450 2D6 (CYP2D6) is proposed to be the conserved I-helix threonine, which is supposed to be involved in dioxygen activation by CYPs. The T309V mutant of CYP2D6 displayed a strong shift from O-dealkylation to N-dealkylation reactions in oxidation of dextromethorphan and 3,4-methylenedioxymethylamphetamine. This may be explained by an elevated ratio of hydroperoxo-iron to oxenoid-iron of the oxygenating species. In consistence, using cumene hydroperoxide, which directly forms the oxenoid-iron, the T309V mutant again selectively catalyzed the O-dealkylation reactions. The changed ratio of oxygenating species can also explain the decreased activity and changed regioselectivity that were observed in 7-methoxy-4-(aminomethyl)-coumarin and bufuralol oxidation, respectively, by the T309V mutant. Interestingly, the T309V mutant always showed a significantly increased, up to 75-fold, higher activity compared to that of the wild-type when using cumene hydroperoxide. These results indicate that T309 in CYP2D6 is involved in maintaining the balance of multiple oxygenating species and thus influences substrate and regioselectivity.
Collapse
Affiliation(s)
- Peter H J Keizers
- Leiden Amsterdam Center for Drug Research (LACDR), Division of Molecular Toxicology, Department of Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Takaya N. Dissimilatory nitrate reduction metabolisms and their control in fungi. J Biosci Bioeng 2005; 94:506-10. [PMID: 16233342 DOI: 10.1016/s1389-1723(02)80187-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2002] [Accepted: 08/26/2002] [Indexed: 10/27/2022]
Abstract
Most fungi grow under aerobic conditions by generating ATP through oxygen respiration. However, they alternatively express two pathways of dissimilatory nitrate reduction in response to environmental oxygen tension when the oxygen supply is insufficient. The fungus Fusarium oxysporum expressed the pathway of respiratory nitrate denitrification that is catalyzed by the sequential reactions of nitrate reductase and nitrite reductase. These enzymes are coupled with ATP generation through the respiratory chain and produce nitric oxide. Fungal nitric oxide reductase uses NADH as the direct electron donor in contrast to bacterial systems and thus might function in regeneration of NAD+ and detoxification of the toxic radical, nitric oxide. Another pathway of nitrate dissimilation by fungi reduces nitrate to ammonium and couples acetogenic reaction with substrate-level phosphorylation. This metabolic mechanism is also in feature of a variety of fungi and it is called ammonia fermentation. Thus, fungi adapt to various aerated conditions using these pathways of nitrate dissimilation in addition to conventional oxygen respiration.
Collapse
Affiliation(s)
- Naoki Takaya
- Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.
| |
Collapse
|
48
|
Hartree–Fock and density functional theory calculations for the reaction mechanism of nitric oxide reductase cytochrome P450nor from Fusarium oxysporum. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2005.06.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
49
|
Praneeth VKK, Haupt E, Lehnert N. Thiolate coordination to Fe(II)–porphyrin NO centers. J Inorg Biochem 2005; 99:940-8. [PMID: 15811511 DOI: 10.1016/j.jinorgbio.2005.02.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2004] [Revised: 02/07/2005] [Accepted: 02/10/2005] [Indexed: 11/22/2022]
Abstract
The interaction of the Fe(II)-porphyrin NO model complex [Fe(TPP)(NO)] (1, TPP=tetraphenylporphyrin) with thiophenolate ligands and tetrahydrothiophene is explored both computationally and experimentally. Complex 1 is reacted with substituted thiophenolates and the obtained six-coordinate adducts of type [Fe(TPP)(SR)(NO)](-) are investigated in solution using electron paramagnetic resonance (EPR) spectroscopy. From the obtained g values and (14)N hyperfine pattern of the NO ligand it is concluded that the interaction of the thiophenolates with the Fe(II) center is weak in comparison to the corresponding 1-methylimidazole adduct. The strength of the Fe-S bond is increased when alkylthiolates are used as evidenced by comparison with the published EPR spectra of ferrous NO adducts in cytochromes P450 and P450nor, which have an axial cysteinate ligand. These results are further evaluated by density functional (DFT) calculations. The six-coordinate model complex [Fe(P)(SMe)(NO)](-) (1-SMe; P=porphine ligand used for the calculations) has an interesting electronic structure where NO acts as a medium strong sigma donor and pi acceptor ligand. Compared to the N-donor adducts with 1-methylimidazole (1-MeIm), etc., donation from the pi(h)( *) orbital of NO to Fe(II) is reduced due to the stronger trans effect of the alkylthiolate ligand. This is reflected by the predicted longer Fe-NO bond length and smaller Fe-NO force constant for 1-SMe compared to the 1-MeIm adduct. Therefore, the Fe(II)-porphyrin NO adducts with trans alkylthiolate coordination have to be described as Fe(II)-NO(radical) systems. The N-O stretching frequency of these complexes is predicted below 1600cm(-1) in agreement with the available experimental data. In addition, 1-SMe has a unique spin density distribution where Fe has a negative spin density of -0.26 from the calculations. The implications of this unusual electronic structure for the reactivity of the Fe(II)-NO alkylthiolate adducts as they occur in cytochrome P450nor are discussed.
Collapse
Affiliation(s)
- V K K Praneeth
- Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
| | | | | |
Collapse
|
50
|
|