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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.
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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
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2
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Ma H, Han XX, Zhao B. Enhanced Raman spectroscopic analysis of protein post-translational modifications. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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3
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Geeraerts Z, Heskin AK, DuBois J, Rodgers KR, Lukat-Rodgers GS. Structure and reactivity of chlorite dismutase nitrosyls. J Inorg Biochem 2020; 211:111203. [PMID: 32768737 PMCID: PMC7749827 DOI: 10.1016/j.jinorgbio.2020.111203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 11/28/2022]
Abstract
Ferric nitrosyl ({FeNO}6) and ferrous nitrosyl ({FeNO}7) complexes of the chlorite dismutases (Cld) from Klebsiella pneumoniae and Dechloromonas aromatica have been characterized using UV-visible absorbance and Soret-excited resonance Raman spectroscopy. Both of these Clds form kinetically stable {FeNO}6 complexes and they occupy a unique region of ν(Fe-NO)/ν(N-O) correlation space for proximal histidine liganded heme proteins, characteristic of weak Fe-NO and N-O bonds. This location is attributed to admixed FeIII-NO character of the {FeNO}6 ground state. Cld {FeNO}6 complexes undergo slow reductive nitrosylation to yield {FeNO}7 complexes. The effects of proximal and distal environment on reductive nitroylsation rates for these dimeric and pentameric Clds are reported. The ν(Fe-NO) and ν(N-O) frequencies for Cld {FeNO}7 complexes reveal both six-coordinate (6c) and five-coordinate (5c) nitrosyl hemes. These 6c and 5c forms are in a pH dependent equilibrium. The 6c and 5c {FeNO}7 Cld frequencies provided positions of both Clds on their respective ν(Fe-NO) vs ν(N-O) correlation lines. The 6c {FeNO}7 complexes fall below (along the ν(Fe-NO) axis) the correlation line that reports hydrogen-bond donation to NNO, which is consistent with a relatively weak Fe-NO bond. Kinetic and spectroscopic evidence is consistent with the 5c {FeNO}7 Clds having NO coordinated on the proximal side of the heme, analogous to 5c {FeNO}7 hemes in proteins known to have NO sensing functions.
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Affiliation(s)
- Zachary Geeraerts
- North Dakota State University, Fargo, ND 58108, United States of America
| | - Alisa K Heskin
- North Dakota State University, Fargo, ND 58108, United States of America
| | - Jennifer DuBois
- Montana State University, Bozeman, MT 59717, United States of America
| | - Kenton R Rodgers
- North Dakota State University, Fargo, ND 58108, United States of America.
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4
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Aono S, Nakajima H. Transcriptional Regulation of Gene Expression by Metalloproteins. PROGRESS IN REACTION KINETICS AND MECHANISM 2019. [DOI: 10.3184/007967400103165128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
FNR and SoxR are transcriptional regulators containing an iron–sulfur cluster. The iron–sulfur cluster in FNR acts as an oxygen sensor by reacting with oxygen. The structural change of the iron–sulfur cluster takes place when FNR senses oxygen, which regulates the transcriptional regulator activity of FNR through the change of the quaternary structure. SoxR contains the [2Fe–2S] cluster that regulates the transcriptional activator activity of SoxR. Only the oxidized SoxR containing the [2Fe–2S]2+ cluster is active as the transcriptional activator. CooA is a transcriptional activator containing a protoheme that acts as a CO sensor. CO is a physiological effector of CooA and regulates the transcriptional activator activity of CooA. In this review, the biochemical and biophysical properties of FNR, SoxR, and CooA are described.
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Affiliation(s)
- Shigetoshi Aono
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Tatsunokuchi, Ishikawa 923-1292, Japan
| | - Hiroshi Nakajima
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Tatsunokuchi, Ishikawa 923-1292, Japan
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5
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Shimizu T, Huang D, Yan F, Stranava M, Bartosova M, Fojtíková V, Martínková M. Gaseous O2, NO, and CO in signal transduction: structure and function relationships of heme-based gas sensors and heme-redox sensors. Chem Rev 2015; 115:6491-533. [PMID: 26021768 DOI: 10.1021/acs.chemrev.5b00018] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Toru Shimizu
- †Department of Cell Biology and Genetics and Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041, China
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
- §Research Center for Compact Chemical System, National Institute of Advanced Industrial Science and Technology (AIST), Sendai 983-8551, Japan
| | - Dongyang Huang
- †Department of Cell Biology and Genetics and Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Fang Yan
- †Department of Cell Biology and Genetics and Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Martin Stranava
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
| | - Martina Bartosova
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
| | - Veronika Fojtíková
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
| | - Markéta Martínková
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
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6
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Servid AE, McKay AL, Davis CA, Garton EM, Manole A, Dobbin PS, Hough MA, Andrew CR. Resonance Raman Spectra of Five-Coordinate Heme-Nitrosyl Cytochromes c′: Effect of the Proximal Heme-NO Environment. Biochemistry 2015; 54:3320-7. [DOI: 10.1021/acs.biochem.5b00227] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amy E. Servid
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Alison L. McKay
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Cherry A. Davis
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Elizabeth M. Garton
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Andreea Manole
- School
of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Paul S. Dobbin
- School
of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Michael A. Hough
- School
of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Colin R. Andrew
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
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Ribeiro CW, Alloing G, Mandon K, Frendo P. Redox regulation of differentiation in symbiotic nitrogen fixation. Biochim Biophys Acta Gen Subj 2014; 1850:1469-78. [PMID: 25433163 DOI: 10.1016/j.bbagen.2014.11.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 10/30/2014] [Accepted: 11/18/2014] [Indexed: 12/22/2022]
Abstract
BACKGROUND Nitrogen-fixing symbiosis between Rhizobium bacteria and legumes leads to the formation of a new organ, the root nodule. The development of the nodule requires the differentiation of plant root cells to welcome the endosymbiotic bacterial partner. This development includes the formation of an efficient vascular tissue which allows metabolic exchanges between the root and the nodule, the formation of a barrier to oxygen diffusion necessary for the bacterial nitrogenase activity and the enlargement of cells in the infection zone to support the large bacterial population. Inside the plant cell, the bacteria differentiate into bacteroids which are able to reduce atmospheric nitrogen to ammonia needed for plant growth in exchange for carbon sources. Nodule functioning requires a tight regulation of the development of plant cells and bacteria. SCOPE OF THE REVIEW Nodule functioning requires a tight regulation of the development of plant cells and bacteria. The importance of redox control in nodule development and N-fixation is discussed in this review. The involvement of reactive oxygen and nitrogen species and the importance of the antioxidant defense are analyzed. MAJOR CONCLUSIONS Plant differentiation and bacterial differentiation are controlled by reactive oxygen and nitrogen species, enzymes involved in the antioxidant defense and antioxidant compounds. GENERAL SIGNIFICANCE The establishment and functioning of nitrogen-fixing symbiosis involve a redox control important for both the plant-bacteria crosstalk and the consideration of environmental parameters. This article is part of a Special Issue entitled Redox regulation of differentiation and de-differentiation.
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Affiliation(s)
- Carolina Werner Ribeiro
- Institut Sophia Agrobiotech, Université de Nice-Sophia Antipolis, 400 Route des Chappes, BP167, F-06903 Sophia Antipolis Cedex, France; Institut Sophia Agrobiotech, INRA UMR 1355, 400 Route des Chappes, BP167, F-06903 Sophia Antipolis Cedex, France; Institut Sophia Agrobiotech, CNRS UMR 7254, 400 Route des Chappes, BP167, F-06903 Sophia Antipolis Cedex, France
| | - Geneviève Alloing
- Institut Sophia Agrobiotech, Université de Nice-Sophia Antipolis, 400 Route des Chappes, BP167, F-06903 Sophia Antipolis Cedex, France; Institut Sophia Agrobiotech, INRA UMR 1355, 400 Route des Chappes, BP167, F-06903 Sophia Antipolis Cedex, France; Institut Sophia Agrobiotech, CNRS UMR 7254, 400 Route des Chappes, BP167, F-06903 Sophia Antipolis Cedex, France
| | - Karine Mandon
- Institut Sophia Agrobiotech, Université de Nice-Sophia Antipolis, 400 Route des Chappes, BP167, F-06903 Sophia Antipolis Cedex, France; Institut Sophia Agrobiotech, INRA UMR 1355, 400 Route des Chappes, BP167, F-06903 Sophia Antipolis Cedex, France; Institut Sophia Agrobiotech, CNRS UMR 7254, 400 Route des Chappes, BP167, F-06903 Sophia Antipolis Cedex, France
| | - Pierre Frendo
- Institut Sophia Agrobiotech, Université de Nice-Sophia Antipolis, 400 Route des Chappes, BP167, F-06903 Sophia Antipolis Cedex, France; Institut Sophia Agrobiotech, INRA UMR 1355, 400 Route des Chappes, BP167, F-06903 Sophia Antipolis Cedex, France; Institut Sophia Agrobiotech, CNRS UMR 7254, 400 Route des Chappes, BP167, F-06903 Sophia Antipolis Cedex, France.
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8
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Matsumura H, Hayashi T, Chakraborty S, Lu Y, Moënne-Loccoz P. The production of nitrous oxide by the heme/nonheme diiron center of engineered myoglobins (Fe(B)Mbs) proceeds through a trans-iron-nitrosyl dimer. J Am Chem Soc 2014; 136:2420-31. [PMID: 24432820 PMCID: PMC4004238 DOI: 10.1021/ja410542z] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Denitrifying NO reductases are transmembrane
protein complexes
that are evolutionarily related to heme/copper terminal oxidases.
They utilize a heme/nonheme diiron center to reduce two NO molecules
to N2O. Engineering a nonheme FeB site within
the heme distal pocket of sperm whale myoglobin has offered well-defined
diiron clusters for the investigation of the mechanism of NO reduction
in these unique active sites. In this study, we use FTIR spectroscopy
to monitor the production of N2O in solution and to show
that the presence of a distal FeBII is not sufficient
to produce the expected product. However, the addition of a glutamate
side chain peripheral to the diiron site allows for 50% of a productive
single-turnover reaction. Unproductive reactions are characterized
by resonance Raman spectroscopy as dinitrosyl complexes, where one
NO molecule is bound to the heme iron to form a five-coordinate low-spin
{FeNO}7 species with ν(FeNO)heme and ν(NO)heme at 522 and 1660 cm–1, and a second NO
molecule is bound to the nonheme FeB site with a ν(NO)FeB at 1755 cm–1. Stopped-flow UV–vis
absorption coupled with rapid-freeze-quench resonance Raman spectroscopy
provide a detailed map of the reaction coordinates leading to the
unproductive iron-nitrosyl dimer. Unexpectedly, NO binding to FeB is kinetically favored and occurs prior to the binding of
a second NO to the heme iron, leading to a (six-coordinate low-spin
heme-nitrosyl/FeB-nitrosyl) transient dinitrosyl complex
with characteristic ν(FeNO)heme at 570 ± 2 cm–1 and ν(NO)FeB at 1755 cm–1. Without the addition of a peripheral glutamate, the dinitrosyl
complex is converted to a dead-end product after the dissociation
of the proximal histidine of the heme iron, but the added peripheral
glutamate side chain in FeBMb2 lowers the rate of dissociation
of the promixal histidine which in turn allows the (six-coordinate
low-spin heme-nitrosyl/FeB-nitrosyl) transient dinitrosyl
complex to decay with production of N2O at a rate of 0.7
s–1 at 4 °C. Taken together, our results support
the proposed trans mechanism of NO reduction in NORs.
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Affiliation(s)
- Hirotoshi Matsumura
- Divison of Environmental & Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , 3181 SW Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
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9
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He C, Neya S, Knipp M. Breaking the Proximal FeII–NHis Bond in Heme Proteins through Local Structural Tension: Lessons from the Heme b Proteins Nitrophorin 4, Nitrophorin 7, and Related Site-Directed Mutant Proteins. Biochemistry 2011; 50:8559-75. [DOI: 10.1021/bi201073t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Chunmao He
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470
Mülheim an der Ruhr, Germany
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical
Sciences, Chiba University, Image-Yayoi,
Chiba 263-8522, Japan
| | - Markus Knipp
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470
Mülheim an der Ruhr, Germany
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10
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Quintas PO, Catarino T, Todorovic S, Turner DL. Highly selective ligand binding by Methylophilus methylotrophus cytochrome c''. Biochemistry 2011; 50:5624-32. [PMID: 21599015 DOI: 10.1021/bi200480a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome c'' (cyt c'') from Methylophilus methylotrophus is unusual insofar as the heme has two axial histidine ligands in the oxidized form but one is detached when the protein is reduced. Despite cyt c'' having an axial site available for binding small ligands, we show here that only NO binds readily to the ferrous cyt c''. Binding of CO, as well as CN(-), on the other hand requires considerable structural reorganization, or reduction of the disulfide bridge close to the heme. Standard free energies for the binding of NO and CO reveal high selectivity of the ferrous cyt c'' for NO, indicating its putative physiological role. In this work, we characterize in detail the kinetics of NO binding and the structural features of the Fe(2+)-NO adduct by stopped-flow and resonance Raman spectroscopy, respectively.
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Affiliation(s)
- Pedro O Quintas
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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11
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Lukat-Rodgers GS, Correia C, Botuyan MV, Mer G, Rodgers KR. Heme-based sensing by the mammalian circadian protein CLOCK. Inorg Chem 2010; 49:6349-65. [PMID: 20666392 DOI: 10.1021/ic902388q] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Heme is emerging as a key player in the synchrony of circadian-coupled transcriptional regulation. Current evidence suggests that levels of circadian-linked transcription are regulated in response to both the availability of intracellular heme and heme-based sensing of carbon monoxide (CO) and possibly nitric oxide (NO). The protein CLOCK is central to the regulation and maintenance of circadian rhythms in mammals. CLOCK comprises two PAS domains, each with a heme binding site. Our studies focus on the functionality of the murine CLOCK PAS-A domain (residues 103-265). We show that CLOCK PAS-A binds iron(III) protoporhyrin IX to form a complex with 1:1 stoichiometry. Optical absorbance and resonance Raman studies reveal that the heme of ferric CLOCK PAS-A is a six-coordinate, low-spin complex whose resonance Raman signature is insensitive to pH over the range of protein stability. Ferrous CLOCK PAS-A is a mixture of five-coordinate, high-spin and six-coordinate, low-spin complexes. Ferrous CLOCK PAS-A forms complexes with CO and NO. Ferric CLOCK PAS-A undergoes reductive nitrosylation in the presence of NO to generate a CLOCK PAS-A-NO, which is a five-coordinate {FeNO}(7) complex. Formation of the highly stable {FeNO}(7) heme complex from either ferrous or ferric heme makes possible the binding of NO at very low concentration, a characteristic of NO sensors. Comparison of the spectroscopic properties and CO-binding kinetics of CLOCK PAS-A with other CO sensor proteins reveals that CLOCK PAS-A exhibits chemical properties consistent with a heme-based gas sensor protein.
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Affiliation(s)
- Gudrun S Lukat-Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, USA
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12
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Catarino T, Pessanha M, De Candia AG, Gouveia Z, Fernandes AP, Pokkuluri PR, Murgida D, Marti MA, Todorovic S, Salgueiro CA. Probing the Chemotaxis Periplasmic Sensor Domains from Geobacter sulfurreducens by Combined Resonance Raman and Molecular Dynamic Approaches: NO and CO Sensing. J Phys Chem B 2010; 114:11251-60. [DOI: 10.1021/jp1029882] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Teresa Catarino
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República (EAN), 2780-157 Oeiras, Portugal, Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal, and
| | - Miguel Pessanha
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República (EAN), 2780-157 Oeiras, Portugal, Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal, and
| | - Ariel G. De Candia
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República (EAN), 2780-157 Oeiras, Portugal, Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal, and
| | - Zélia Gouveia
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República (EAN), 2780-157 Oeiras, Portugal, Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal, and
| | - Ana P. Fernandes
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República (EAN), 2780-157 Oeiras, Portugal, Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal, and
| | - P. Raj Pokkuluri
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República (EAN), 2780-157 Oeiras, Portugal, Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal, and
| | - Daniel Murgida
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República (EAN), 2780-157 Oeiras, Portugal, Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal, and
| | - Marcelo A. Marti
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República (EAN), 2780-157 Oeiras, Portugal, Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal, and
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República (EAN), 2780-157 Oeiras, Portugal, Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal, and
| | - Carlos A. Salgueiro
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República (EAN), 2780-157 Oeiras, Portugal, Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal, and
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13
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Scheidt WR, Barabanschikov A, Pavlik JW, Silvernail NJ, Sage JT. Electronic structure and dynamics of nitrosyl porphyrins. Inorg Chem 2010; 49:6240-52. [PMID: 20666384 PMCID: PMC2919577 DOI: 10.1021/ic100261b] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitric oxide (NO) is a signaling molecule employed to regulate essential physiological processes. Thus, there is great interest in understanding the interaction of NO with heme, which is found at the active site of many proteins that recognize NO, as well as those involved in its creation and elimination. We summarize what we have learned from investigations of the structure, vibrational properties, and conformational dynamics of NO complexes with ferrous porphyrins, as well as computational investigations in support of these experimental studies. Multitemperature crystallographic data reveal variations in the orientational disorder of the nitrosyl ligand. In some cases, equilibria among NO orientations can be analyzed using the van't Hoff relationship and the free energy and enthalpy of the solid-state transitions evaluated experimentally. Density functional theory (DFT) calculations predict that intrinsic barriers to torsional rotation are smaller than thermal energies at physiological temperatures, and the coincidence of observed NO orientations with minima in molecular mechanics potentials indicates that nonbonded interactions with other chemical groups control the conformational freedom of the bound NO. In favorable cases, reduced disorder at low temperatures exposes subtle structural features including off-axis tilting of the Fe-NO bond and anisotropy of the equatorial Fe-N bonds. We also present the results of nuclear resonance vibrational spectroscopy measurements on oriented single crystals of [Fe(TPP)(NO)] and [Fe(TPP)(1-MeIm)(NO)]. These describe the anisotropic vibrational motion of iron in five- and six-coordinate heme-NO complexes and reveal vibrations of all Fe-ligand bonds as well as low-frequency molecular distortions associated with the doming of the heme upon ligand binding. A quantitative comparison with predicted frequencies, amplitudes, and directions facilitates identification of the vibrational modes but also suggests that commonly used DFT functionals are not fully successful at capturing the trans interaction between the axial NO and imidazole ligands. This supports previous conclusions that heme-NO complexes exhibit an unusual degree of variability with respect to the computational method, and we speculate that this variability hints at a genuine electronic instability that a protein can exploit to tune its reactivity. We anticipate that ongoing characterization of heme-NO complexes will deepen our understanding of their structure, dynamics, and reactivity.
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Affiliation(s)
- W. Robert Scheidt
- To whom correspondence should be addressed: WRS: , Fax (574) 631-6652; JTS , FAX (617)-373-2943
| | | | | | | | - J. Timothy Sage
- To whom correspondence should be addressed: WRS: , Fax (574) 631-6652; JTS , FAX (617)-373-2943
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14
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Ouellet H, Lang J, Couture M, Ortiz de Montellano PR. Reaction of Mycobacterium tuberculosis cytochrome P450 enzymes with nitric oxide. Biochemistry 2009; 48:863-72. [PMID: 19146393 DOI: 10.1021/bi801595t] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
During the initial growth infection stage of Mycobacterium tuberculosis (Mtb), (*)NO produced by host macrophages inhibits heme-containing terminal cytochrome oxidases, inactivates iron/sulfur proteins, and promotes entry into latency. Here we evaluate the potential of (*)NO as an inhibitor of Mtb cytochrome P450 enzymes, as represented by CYP130, CYP51, and the two previously uncharacterized enzymes CYP125 and CYP142. Using UV-visible absorption, resonance Raman, and stopped-flow spectroscopy, we investigated the reactions of (*)NO with these heme proteins in their ferric resting form. (*)NO coordinates tightly to CYP125 and CYP142 (submicromolar) and with a lower affinity (micromolar) to CYP130 and CYP51. Anaerobic reduction of the ferric-NO species with sodium dithionite led to the formation of two spectrally distinct classes of five-coordinate ferrous-NO complexes. Exposure of these species to O(2) revealed that the ferrous-NO forms of CYP125 and CYP142 are labile and convert back to the ferric state within a few minutes, whereas ferrous CYP130 and CYP51 bind (*)NO almost irreversibly. This work clearly indicates that, at physiological concentrations (approximately 1 microM), (*)NO would impair the activity of CYP130 and CYP51, whereas CYP125 and CYP142 are more resistant. Selective P450 inhibition may contribute to the inhibitory effects of (*)NO on Mtb growth.
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Affiliation(s)
- Hugues Ouellet
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94158-2517, USA
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15
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Ultrafast ligand binding dynamics in the active site of native bacterial nitric oxide reductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:919-24. [DOI: 10.1016/j.bbabio.2008.03.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 03/03/2008] [Accepted: 03/19/2008] [Indexed: 11/18/2022]
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16
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Ioanoviciu A, Yukl ET, Moënne-Loccoz P, Ortiz de Montellano PR. DevS, a heme-containing two-component oxygen sensor of Mycobacterium tuberculosis. Biochemistry 2007; 46:4250-60. [PMID: 17371046 PMCID: PMC2518089 DOI: 10.1021/bi602422p] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis can exist in the actively growing state of the overt disease or in a latent quiescent state that can be induced, among other things, by anaerobiosis. Eradication of the latent state is particularly difficult with the available drugs and requires prolonged treatment. DevS is a member of the DevS-DevR two-component regulatory system that is thought to mediate the cellular response to anaerobiosis. Here we report the cloning, expression, and initial characterization of a truncated version of DevS (DevS642) containing only the N-terminal GAF sensor domain (GAF-A) and of the full-length protein DevS. The DevS truncated construct quantitatively binds heme in a 1:1 stoichiometry, and the complex of the protein with ferrous heme reversibly binds O2, NO, and CO. UV-vis and resonance Raman spectroscopy of the wild-type protein and the H149A mutant confirm that His149 is the proximal ligand to the heme iron atom. While the heme-CO complex is present as two conformers in the GAF-A domain, a single set of [Fe-C-O] vibrations is observed with the full-length protein, suggesting that interactions between domains within DevS influence the distal pocket environment of the heme in the GAF-A domain.
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Affiliation(s)
- Alexandra Ioanoviciu
- Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94158-2517
| | - Erik T. Yukl
- Department of Environmental & Biomolecular Systems, 20,000 NW Walker Road, OGI School of Science and Engineering, Oregon Health & Sciences University, Beaverton, Oregon 97006-8921
| | - Pierre Moënne-Loccoz
- Department of Environmental & Biomolecular Systems, 20,000 NW Walker Road, OGI School of Science and Engineering, Oregon Health & Sciences University, Beaverton, Oregon 97006-8921
| | - Paul R. Ortiz de Montellano
- Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94158-2517
- To whom editorial correspondence should be addressed: Dr. Paul Ortiz de Montellano, University of California, Genentech Hall GH-N572D, 600 16 Street, Box 2280, San Francisco, CA 94158-2517, TEL: (415) 476-2903, FAX: (415) 502-4728, e-mail:
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17
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Dai RJ, Ke SC. Detection and determination of the {Fe(NO)(2)} core vibrational features in dinitrosyl-iron complexes from experiment, normal coordinate analysis, and density functional theory: an avenue for probing the nitric oxide oxidation state. J Phys Chem B 2007; 111:2335-46. [PMID: 17295535 DOI: 10.1021/jp066964f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As it is now well-established that nitric oxide plays an important role in many physiological processes, there is a renewed interest in dinitrosyl-iron complexes (DNICs). The question concerning the electronic structure of DNICs circles around the formal oxidation states of the iron and nitric oxide of the Fe(NO)2 core. Previous infrared measurements of nu(NO) alone point out inconsistencies in assigning electron configurations and charges on metals, inherent from the measurement of one parameter external to the metal. This work represents the first experimental and theoretical attempt to assign vibrational modes for the {Fe(NO)2}9 core of DNICs. The following complexes are investigated, [PPN][S5Fe(NO)2] (1), [PPN][Se5Fe(NO)2] (2), [PPN][(SPh)2Fe(NO)2] (3), and [PPN][(SePh)2Fe(NO)2] (4). The analysis of isotopically edited Raman data together with normal coordinate calculation permitted assignment of nu(NO) and nu(Fe-NO) stretching and delta(Fe-N-O) bending modes in these complexes. The assignments proposed are the first ever reported for the DNICs; a comparison of nu(NO) and nu(Fe-NO) stretching frequencies in DNICs is now feasible. The Fe(NO)2 core electronic configuration in these complexes is described as {Fe1+(*NO)2}. Results from 1 and 3 have been complemented by density functional theory (DFT) frequency calculations. In addition to providing a reasonably correct account of the observed frequencies, DFT calculations also give a good account of the frequency shifts upon 15NO substitution providing the first link between DFT and Raman spectroscopies for DNICs. Through the use of a combination of NO intraligand and metal-ligand vibrational data for the Fe(NO)2 core, normal coordinate analysis gives a NO stretching force constant, which compared to molecular NO gas, is significantly reduced for all four complexes. The hybrid U-B3LYP/6-311++G(3d,2p) density functional method has been employed to analyze the molecular orbital compositions of predominantly NO orbitals based on the crystal structure of complex 1. The molecular orbital not only revealed the bonding nature of the {Fe(NO)2}9 core but also provided a qualitative correct account of the observed low NO vibrational frequencies. The calculation shows that the NO is involved in a strong donor bonding interaction with the Fe1+. This donor bonding interaction involves the 5sigma molecular orbital of the NO, which is sigma-bonding with respect to the intramolecular NO bond, and removal of electron density from this orbital destabilizes the NO bond. Though it is too ambiguous to extrapolate a nu(Fe-NO)/nu(NO) correlation line for {Fe(NO)2}9 DNICs based only on the data reported here, the feasibility of using a vibrational systematics diagram to extract the electron configurations and charges on metals is demonstrated based on the vibrational data available in the literature for iron-nitrosyl complexes. The data provided here can be used as a model for the determination of effective charges on iron and the bonding of nitric oxides to metals in DNICs.
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Affiliation(s)
- Ruei Jang Dai
- Physics Department, National Dong Hwa University, Hualien 974-01, Taiwan
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18
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Chartier F, Couture M. Interactions between substrates and the haem-bound nitric oxide of ferric and ferrous bacterial nitric oxide synthases. Biochem J 2007; 401:235-45. [PMID: 16970546 PMCID: PMC1698664 DOI: 10.1042/bj20060913] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Revised: 09/11/2006] [Accepted: 09/14/2006] [Indexed: 11/17/2022]
Abstract
We report here the resonance Raman spectra of the FeIII-NO and FeII-NO complexes of the bacterial NOSs (nitric oxide synthases) from Staphylococcus aureus and Bacillus subtilis. The haem-NO complexes of these bacterial NOSs displayed Fe-N-O frequencies similar to those of the mammalian NOSs, in presence and absence of L-arginine, indicating that haem-bound NO and L-arginine had similar haem environments in bacterial and mammalian NOSs. The only notable difference between the two types of NOS was the lack of change in Fe-N-O frequencies of the FeIII-NO complexes upon (6R) 5,6,7,8-tetrahydro-L-biopterin binding to bacterial NOSs. We report, for the first time, the characterization of NO complexes with NOHA (N(omega)-hydroxy-L-arginine), the substrate used in the second half of the catalytic cycle of NOSs. In the FeIII-NO complexes, both L-arginine and NOHA induced the Fe-N-O bending mode at nearly the same frequency as a result of a steric interaction between the substrates and the haem-bound NO. However, in the FeII-NO complexes, the Fe-N-O bending mode was not observed and the nu(Fe-NO) mode displayed a 5 cm(-1) higher frequency in the complex with NOHA than in the complex with L-arginine as a result of direct interactions that probably involve hydrogen bonds. The different behaviour of the substrates in the FeII-NO complexes thus reveal that the interactions between haem-bound NO and the substrates are finely tuned by the geometry of the Fe-ligand structure and are relevant to the use of the FeII-NO complex as a model of the oxygenated complex of NOSs.
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Key Words
- l-arginine
- haem
- nω-hydroxy-l-arginine (noha)
- nitric oxide synthase (nos)
- resonance raman spectroscopy
- 5c, 5-co-ordinated
- 6c, 6-co-ordinated
- bsnos, bacillus subtilis nitric oxide synthase
- drnos, deinococcus radiodurans nos
- dtt, dithiothreitol
- enos, endothelial nos
- feiii, ferric form
- feii, ferrous form
- gsnos, geobacillus stearothermophilus nos
- h4b, (6r) 5,6,7,8-tetrahydro-l-biopterin
- inos, inducible nos
- nnos, neuronal nos
- noha, nω-hydroxy-l-arginine
- nosox, oxygenase domain of nos
- sanos, staphylococcus aureus nos
- thf, tetrahydrofolate
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Affiliation(s)
- François J. M. Chartier
- Département de Biochimie et de Microbiologie, and Centre de Recherche sur la fonction, la structure et l'ingénierie des protéines (CREFSIP), Université Laval, Québec, Canada
| | - Manon Couture
- Département de Biochimie et de Microbiologie, and Centre de Recherche sur la fonction, la structure et l'ingénierie des protéines (CREFSIP), Université Laval, Québec, Canada
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19
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Boon EM, Davis JH, Tran R, Karow DS, Huang SH, Pan D, Miazgowicz MM, Mathies RA, Marletta MA. Nitric oxide binding to prokaryotic homologs of the soluble guanylate cyclase beta1 H-NOX domain. J Biol Chem 2006; 281:21892-21902. [PMID: 16728401 DOI: 10.1074/jbc.m600557200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The heme cofactor in soluble guanylate cyclase (sGC) is a selective receptor for NO, an important signaling molecule in eukaryotes. The sGC heme domain has been localized to the N-terminal 194 amino acids of the beta1 subunit of sGC and is a member of a family of conserved hemoproteins, called the H-NOX family (Heme-Nitric Oxide and/or OXygen-binding domain). Three new members of this family have now been cloned and characterized, two proteins from Legionella pneumophila (L1 H-NOX and L2 H-NOX) and one from Nostoc punctiforme (Np H-NOX). Like sGC, L1 H-NOX forms a 5-coordinate Fe(II)-NO complex. However, both L2 H-NOX and Np H-NOX form temperature-dependent mixtures of 5- and 6-coordinate Fe(II)-NO complexes; at low temperature, they are primarily 6-coordinate, and at high temperature, the equilibrium is shifted toward a 5-coordinate geometry. This equilibrium is fully reversible with temperature in the absence of free NO. This process is analyzed in terms of a thermally labile proximal Fe(II)-His bond and suggests that in both the 5- and 6-coordinate Fe(II)-NO complexes of L2 H-NOX and Np H-NOX, NO is bound in the distal heme pocket of the H-NOX fold. NO dissociation kinetics for L1 H-NOX and L2 H-NOX have been determined and support a model in which NO dissociates from the distal side of the heme in both 5- and 6-coordinate complexes.
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Affiliation(s)
- Elizabeth M Boon
- Department of Chemistry, University of California, Berkeley, California 94720
| | - Joseph H Davis
- Department of Chemistry, University of California, Berkeley, California 94720
| | - Rosalie Tran
- Department of Chemistry, University of California, Berkeley, California 94720
| | - David S Karow
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Shirley H Huang
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Duohai Pan
- Department of Chemistry, University of California, Berkeley, California 94720
| | | | - Richard A Mathies
- Department of Chemistry, University of California, Berkeley, California 94720; Division of Physical Biosciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Michael A Marletta
- Department of Chemistry, University of California, Berkeley, California 94720; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720; Division of Physical Biosciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720.
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20
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Lansky IB, Lukat-Rodgers GS, Block D, Rodgers KR, Ratliff M, Wilks A. The Cytoplasmic Heme-binding Protein (PhuS) from the Heme Uptake System of Pseudomonas aeruginosa Is an Intracellular Heme-trafficking Protein to the δ-Regioselective Heme Oxygenase. J Biol Chem 2006; 281:13652-13662. [PMID: 16533806 DOI: 10.1074/jbc.m600824200] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The uptake and utilization of heme as an iron source is a receptor-mediated process in bacterial pathogens and involves a number of proteins required for internalization and degradation of heme. In the following report we provide the first in-depth spectroscopic and functional characterization of a cytoplasmic heme-binding protein PhuS from the opportunistic pathogen Pseudomonas aeruginosa. Spectroscopic characterization of the heme-PhuS complex at neutral pH indicates that the heme is predominantly six-coordinate low spin. However, the resonance Raman spectra and global fit analysis of the UV-visible spectra show that at all pH values between 6 and 10 three distinct species are present to varying degrees. The distribution of the heme across multiple spin states and coordination number highlights the flexibility of the heme environment. We provide further evidence that the cytoplasmic heme-binding proteins, contrary to previous reports, are not heme oxygenases. The degradation of the heme-PhuS complex in the presence of a reducing agent is a result of H2O2 formed by direct reduction of molecular oxygen and does not yield biliverdin. In contrast, the heme-PhuS complex is an intracellular heme trafficking protein that specifically transfers heme to the previously characterized iron-regulated heme oxygenase pa-HO. Surface plasmon resonance experiments confirm that the transfer of heme is driven by a specific protein-protein interaction. This data taken together with the spectroscopic characterization is consistent with a protein that functions to shuttle heme within the cell.
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Affiliation(s)
- Ila B Lansky
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - Gudrun S Lukat-Rodgers
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105-5516
| | - Darci Block
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105-5516
| | - Kenton R Rodgers
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105-5516
| | - Melanie Ratliff
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - Angela Wilks
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201.
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21
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Li D, Hayden EY, Panda K, Stuehr DJ, Deng H, Rousseau DL, Yeh SR. Regulation of the monomer-dimer equilibrium in inducible nitric-oxide synthase by nitric oxide. J Biol Chem 2006; 281:8197-204. [PMID: 16421101 DOI: 10.1074/jbc.m507328200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The oxygenase domain of inducible nitric-oxide synthase exists as a functional tight homodimer in the presence of the substrate L-arginine and the cofactor tetrahydrobiopterin (H4B). In the absence of H4B, the enzyme is a mixture of monomer and loose dimer. We show that exposure of H4B-free enzyme to NO induces dissociation of the loose dimer into monomers in a reaction that follows single exponential decay kinetics with a lifetime of approximately 300 min. It is followed by a faster autoreduction reaction of the heme iron with a lifetime of approximately 30 min and the concurrent breakage of the proximal iron-thiolate bond, forming a five-coordinate NO-bound ferrous species. Mass spectrometry revealed that the NO-induced monomerization is associated with intramolecular disulfide bond formation between Cys104 and Cys109, located in the zinc-binding motif. The regulatory effect of NO as a dimer inhibitor is discussed in the context of the structure/function relationships of this enzyme.
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Affiliation(s)
- David Li
- Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA
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22
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Konishi K, Ohta T, Oinuma KI, Hashimoto Y, Kitagawa T, Kobayashi M. Discovery of a reaction intermediate of aliphatic aldoxime dehydratase involving heme as an active center. Proc Natl Acad Sci U S A 2006; 103:564-8. [PMID: 16407114 PMCID: PMC1334632 DOI: 10.1073/pnas.0505412103] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recently, we discovered an intriguing hemoprotein [aliphatic aldoxime dehydratase (OxdA)] that catalyzes the dehydration of aliphatic aldoximes [R-CH=N-OH] to the corresponding nitriles [R-C identical withN] in the industrial Pseudomonas chlororaphis B23 strain. Unlike the utilization of H(2)O(2) or O(2) as a mediator of the catalysis by other heme-containing enzymes (e.g., P450), OxdA is notable for the direct binding of a substrate to the heme iron, experimental evidence of which was obtained here by means of resonance Raman (RR) analysis with an isotope technique. We found that the addition of a large amount of butyraldoxime (final concentration, 200 mM) to ferrous OxdA with a low enzyme concentration (final concentration, 5 muM) yields a long-lived OxdA-substrate complex (named OS-II), whose UV-vis spectrum is different from the corresponding spectra of the OxdA-substrate complex I and CO-bound, ferrous, and ferric forms of OxdA. Intriguingly, the RR analysis demonstrated that OS-II includes a highly oxidized heme with strong bonding between a substrate and the heme iron, as judged from the heme oxidation state marker nu(4) band at 1,379 cm(-1) and the (15)N-isotope-substituted butyraldoxime sensitive band at 857 cm(-1) in the RR spectra. It is noteworthy that OS-II has a highly oxidized heme like the ferryl-oxo heme species (e.g., compound II) formed by some general hemoproteins, although the function of OxdA is different from those (transport of electrons, transport of oxygen, sensing of oxygen or carbon monoxide, and catalysis of redox reactions) of general hemoproteins.
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Affiliation(s)
- Kazunobu Konishi
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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23
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Karow DS, Pan D, Davis JH, Behrends S, Mathies RA, Marletta MA. Characterization of functional heme domains from soluble guanylate cyclase. Biochemistry 2005; 44:16266-74. [PMID: 16331987 PMCID: PMC2572136 DOI: 10.1021/bi051601b] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Soluble guanylate cyclase (sGC) is a heterodimeric, nitric oxide (NO)-sensing hemoprotein composed of two subunits, alpha1 and beta1. NO binds to the heme cofactor in the beta1 subunit, forming a five-coordinate NO complex that activates the enzyme several hundred-fold. In this paper, the heme domain has been localized to the N-terminal 194 residues of the beta1 subunit. This fragment represents the smallest construct of the beta1 subunit that retains the ligand-binding characteristics of the native enzyme, namely, tight affinity for NO and no observable binding of O(2). A functional heme domain from the rat beta2 subunit has been localized to the first 217 amino acids beta2(1-217). These proteins are approximately 40% identical to the rat beta1 heme domain and form five-coordinate, low-spin NO complexes and six-coordinate, low-spin CO complexes. Similar to sGC, these constructs have a weak Fe-His stretch [208 and 207 cm(-)(1) for beta1(1-194) and beta2(1-217), respectively]. beta2(1-217) forms a CO complex that is very similar to sGC and has a high nu(CO) stretching frequency at 1994 cm(-)(1). The autoxidation rate of beta1(1-194) was 0.073/min, while the beta2(1-217) was substantially more stable in the ferrous form with an autoxidation rate of 0.003/min at 37 degrees C. This paper has identified and characterized the minimum functional ligand-binding heme domain derived from sGC, providing key details toward a comprehensive characterization.
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Affiliation(s)
- David S Karow
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
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24
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Rodgers KR, Lukat-Rodgers GS. Insights into heme-based O2 sensing from structure-function relationships in the FixL proteins. J Inorg Biochem 2005; 99:963-77. [PMID: 15811514 DOI: 10.1016/j.jinorgbio.2005.02.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Revised: 02/08/2005] [Accepted: 02/14/2005] [Indexed: 10/25/2022]
Abstract
FixL proteins are bacterial heme-containing signal transduction proteins responsible for sensing the O(2) concentration in the organism's environment. In Sinorhizobium meliloti FixL is a protein histidine kinase that, together with its response regulator FixJ, constitute an oxygen-sensitive switch for regulation of the organism's nitrogen fixation and microaerobic respiration genes. The O(2) sensitivity of the switch is such that it transitions during the process of symbiosis in alfalfa roots. Bradyrhizobium japonicum FixL similarly regulates microaerobic and anaerobic respiration genes during symbiosis in soybean roots. FixLs responds to low oxygen concentrations with increased autophosphorylation activity of their kinase domains. The phosphorylated FixL provides a phosphoryl group to FixJ within a FixLJ complex. The phosphorylated FixJs are transcriptionally active toward their target genes. The FixL kinase domain is inhibited when the heme in FixL is oxygenated. Kinetic and thermodynamic studies of ligand binding to both ferrous and ferric FixLs have shown a generally low affinity for ligands relative to myoglobins. These relatively low ligand affinities are attributable almost completely to diminished rates of ligand binding. The heme and its environment in liganded and unliganded FixLs have been characterized by UV-visible spectroscopy, resonance Raman spectroscopy, EXAFS, and X-ray crystallography. These studies have revealed that in the purified proteins, the heme is converted from a six-coordinate low spin state to a five-coordinate high spin state upon O(2) release. Comparisons of spectroscopic and structural characteristics of deoxyFixL with oxyFixL, met-FixL-CN, FixL-CO, and FixL-NO complexes indicate that distal affects in the heme pocket are, at least in part, responsible for communicating the ligation state of the heme to the kinase domain. The mechanisms by which ligand binding events are communicated from the heme to the kinase domain involves propagation and/or amplification of the ligation-coupled conformational transitions of the heme and its immediate protein environment. More recently, time-resolved experiments examining the nonequilibrium, ligand-coupled dynamics initiated by O(2), CO, and NO photolysis from the corresponding FixL complexes have begun to shed light on the landscape of the switching coordinate. Current thinking and understanding of the mechanism for signal transduction in the FixLJ systems are discussed in the context of these physical investigations.
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Affiliation(s)
- Kenton R Rodgers
- Department of Chemistry and Molecular Biology, North Dakota State University, Ladd Hall, Fargo, ND 58105-5516, USA.
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25
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Balland V, Bouzhir-Sima L, Kiger L, Marden MC, Vos MH, Liebl U, Mattioli TA. Role of Arginine 220 in the Oxygen Sensor FixL from Bradyrhizobium japonicum. J Biol Chem 2005; 280:15279-88. [PMID: 15711013 DOI: 10.1074/jbc.m413928200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the heme-based oxygen sensor protein FixL, conformational changes induced by oxygen binding to the heme sensor domain regulate the activity of a neighboring histidine kinase, eventually restricting expression of specific genes to hypoxic conditions. The conserved arginine 220 residue is suggested to play a key role in the signal transduction mechanism. To obtain detailed insights into the role of this residue, we replaced Arg(220) by histidine (R220H), glutamine (R220Q), glutamate (R220E), and isoleucine (R220I) in the heme domain FixLH from Bradyrhizobium japonicum. These mutations resulted in dramatic changes in the O(2) affinity with K(d) values in the order R220I < R220Q < wild type < R220H. For the R220H and R220Q mutants, residue 220 interacts with the bound O(2) or CO ligands, as seen by resonance Raman spectroscopy. For the oxy-adducts, this H-bond modifies the pi acidity of the O(2) ligand, and its strength is correlated with the back-bonding-sensitive nu(4) frequency, the k(off) value for O(2) dissociation, and heme core-size conformational changes. This effect is especially strong for the wild-type protein where Arg(220) is, in addition, positively charged. These observations strongly suggest that neither strong ligand fixation nor the displacement of residue 220 into the heme distal pocket are solely responsible for the reported heme conformational changes associated with kinase activity regulation, but that a significant decrease of the heme pi(*) electron density because of strong back-bonding toward the oxygen ligand also plays a key role.
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Affiliation(s)
- Véronique Balland
- Laboratoire de Biophysique du Stress Oxydant, SBE/DBJC and CNRS URA 2096, CEA/Saclay, 91191 Gif-sur-Yvette cedex, France
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26
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Leu BM, Zgierski MZ, Wyllie GRA, Scheidt WRE, Sturhahn W, Alp EE, Durbin SM, Sage JT. Quantitative vibrational dynamics of iron in nitrosyl porphyrins. J Am Chem Soc 2004; 126:4211-27. [PMID: 15053610 PMCID: PMC1570756 DOI: 10.1021/ja038526h] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We use quantitative experimental and theoretical approaches to characterize the vibrational dynamics of the Fe atom in porphyrins designed to model heme protein active sites. Nuclear resonance vibrational spectroscopy (NRVS) yields frequencies, amplitudes, and directions for 57Fe vibrations in a series of ferrous nitrosyl porphyrins, which provide a benchmark for evaluation of quantum chemical vibrational calculations. Detailed normal mode predictions result from DFT calculations on ferrous nitrosyl tetraphenylporphyrin Fe(TPP)(NO), its cation [Fe(TPP)(NO)]+, and ferrous nitrosyl porphine Fe(P)(NO). Differing functionals lead to significant variability in the predicted Fe-NO bond length and frequency for Fe(TPP)(NO). Otherwise, quantitative comparison of calculated and measured Fe dynamics on an absolute scale reveals good overall agreement, suggesting that DFT calculations provide a reliable guide to the character of observed Fe vibrational modes. These include a series of modes involving Fe motion in the plane of the porphyrin, which are rarely identified using infrared and Raman spectroscopies. The NO binding geometry breaks the four-fold symmetry of the Fe environment, and the resulting frequency splittings of the in-plane modes predicted for Fe(TPP)(NO) agree with observations. In contrast to expectations of a simple three-body model, mode energy remains localized on the FeNO fragment for only two modes, an N-O stretch and a mode with mixed Fe-NO stretch and FeNO bend character. Bending of the FeNO unit also contributes to several of the in-plane modes, but no primary FeNO bending mode is identified for Fe(TPP)(NO). Vibrations associated with hindered rotation of the NO and heme doming are predicted at low frequencies, where Fe motion perpendicular to the heme is identified experimentally at 73 and 128 cm-1. Identification of the latter two modes is a crucial first step toward quantifying the reactive energetics of Fe porphyrins and heme proteins.
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Affiliation(s)
- Bogdan M. Leu
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA 02115
| | - Marek Z. Zgierski
- Steacie Institute for Molecular Science, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
| | - Graeme R. A. Wyllie
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - W. Rob ert Scheidt
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Wolfgang Sturhahn
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - E. Ercan Alp
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | | | - J. Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA 02115
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Igarashi J, Sato A, Kitagawa T, Yoshimura T, Yamauchi S, Sagami I, Shimizu T. Activation of heme-regulated eukaryotic initiation factor 2alpha kinase by nitric oxide is induced by the formation of a five-coordinate NO-heme complex: optical absorption, electron spin resonance, and resonance raman spectral studies. J Biol Chem 2004; 279:15752-62. [PMID: 14752110 DOI: 10.1074/jbc.m310273200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Heme-regulated eukaryotic initiation factor 2alpha kinase (HRI) regulates the synthesis of hemoglobin in reticulocytes in response to heme availability. HRI contains a tightly bound heme at the N-terminal domain. Earlier reports show that nitric oxide (NO) regulates HRI catalysis. However, the mechanism of this process remains unclear. In the present study, we utilize in vitro kinase assays, optical absorption, electron spin resonance (ESR), and resonance Raman spectra of purified full-length HRI for the first time to elucidate the regulation mechanism of NO. HRI was activated via heme upon NO binding, and the Fe(II)-HRI(NO) complex displayed 5-fold greater eukaryotic initiation factor 2alpha kinase activity than the Fe(III)-HRI complex. The Fe(III)-HRI complex exhibited a Soret peak at 418 nm and a rhombic ESR signal with g values of 2.49, 2.28, and 1.87, suggesting coordination with Cys as an axial ligand. Interestingly, optical absorption, ESR, and resonance Raman spectra of the Fe(II)-NO complex were characteristic of five-coordinate NO-heme. Spectral findings on the coordination structure of full-length HRI were distinct from those obtained for the isolated N-terminal heme-binding domain. Specifically, six-coordinate NO-Fe(II)-His was observed but not Cys-Fe(III) coordination. It is suggested that significant conformational change(s) in the protein induced by NO binding to the heme lead to HRI activation. We discuss the role of NO and heme in catalysis by HRI, focusing on heme-based sensor proteins.
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Affiliation(s)
- Jotaro Igarashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
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28
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Taguchi S, Matsui T, Igarashi J, Sasakura Y, Araki Y, Ito O, Sugiyama S, Sagami I, Shimizu T. Binding of Oxygen and Carbon Monoxide to a Heme-regulated Phosphodiesterase from Escherichia coli. J Biol Chem 2004; 279:3340-7. [PMID: 14612459 DOI: 10.1074/jbc.m301013200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The heme-regulated phosphodiesterase, Ec DOS, is a redox sensor that uses the heme in its PAS domain to regulate catalysis. The rate of O(2) association (k(on)) with full-length Ec DOS is extremely slow at 0.0019 microM(-1) s(-1), compared with >9.5 microM(-1) s(-1) for 6-coordinated globin-type hemoproteins, as determined by the stopped-flow method. This rate is dramatically increased (up to 16-fold) in the isolated heme-bound PAS domain. Dissociation constants (K(d)) calculated from the kinetic parameters are 340 and 20 microm for the full-length wild-type enzyme and its isolated PAS domain, respectively. Mutations at Met-95 in the isolated PAS domain, which may be a heme axial ligand in the Fe(II) complex, lead to a further increase in the k(on) value by more than 30-fold, and consequently, a decrease in the K(d) value to less than 1 microM. The k(on) value for CO binding to the full-length wild-type enzyme is also very low (0.00081 microM(-1) s(-1)). The kinetics of CO binding to the isolated PAS domain and its mutants are similar to those observed for O(2). However, the K(d) values for CO are considerably lower than those for O(2).
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Affiliation(s)
- Sue Taguchi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
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29
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Martí MA, Scherlis DA, Doctorovich FA, Ordejón P, Estrin DA. Modulation of the NO trans effect in heme proteins: implications for the activation of soluble guanylate cyclase. J Biol Inorg Chem 2003; 8:595-600. [PMID: 12644910 DOI: 10.1007/s00775-003-0452-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2002] [Accepted: 02/18/2003] [Indexed: 11/29/2022]
Abstract
The binding of NO to the iron heme in guanylate cyclase and other heme proteins induces the cleavage of the proximal histidine bonded to the metal. In this study we assess by means of density functional theory (DFT) electronic structure calculations the role of H-bonding to histidine in the modulation of this effect. We have considered in the first place a model of the isolated active site coordinated with imidazole and imidazolate to mimic the effects of a very strong H-bond. We have also investigated four selected ferrous heme proteins with different proximal histidine environments: the O(2) sensing FixL, horseradish peroxidase C, and the alpha and beta subunits of human hemoglobin. Our results indicate that polarization and charge transfer effects associated with H-bonding to the proximal histidine play a fundamental role in the modulation of the NO trans effect in heme proteins. We also find computational evidence suggesting that protein structural constraints may affect significantly the cleavage of the Fe-His bond.
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Affiliation(s)
- Marcelo A Martí
- Departamento de Química Inorgánica, Analítica y Química Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II (C1428EHA), Buenos Aires, Argentina
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30
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Akimoto S, Tanaka A, Nakamura K, Shiro Y, Nakamura H. O2-specific regulation of the ferrous heme-based sensor kinase FixL from Sinorhizobium meliloti and its aberrant inactivation in the ferric form. Biochem Biophys Res Commun 2003; 304:136-42. [PMID: 12705897 DOI: 10.1016/s0006-291x(03)00556-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
FixL, a rhizobial heme-based O2-sensing histidine kinase, catalyzes autophosphorylation in the deoxy form at low O2 tension, while the kinase activity is inhibited in the case of the O2-bound form. The present study unambiguously shows that the binding of CO and NO does not significantly inhibit the kinase activity of dithiothreitol (DTT)-reduced ferrous FixL from Sinorhizobium meliloti, which is inconsistent with the spin state mechanism previously reported. Kinase inactivation is caused by aberrant disulfide (S-S) bond formation at Cys301 in the ferric homodimer, which explains these contradictory observations. The addition of DTT cleaved the S-S bond, leading to restoration of kinase activity in the ferric form as well as heme reduction, but, sodium hydrosulfite treatment produced the kinase-inactive deoxy form without S-S cleavage. On the basis of these experimental results, it can be concluded that ferrous FixL discriminates O2 from CO and NO, and signals the O2-bound state by downregulating the phosphoryl transfer reaction.
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Affiliation(s)
- Satoru Akimoto
- RIKEN Harima Institute/SPring-8, Mikazuki, 679-5148, Hyogo, Japan
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31
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Liebl U, Bouzhir-Sima L, Negrerie M, Martin JL, Vos MH. Ultrafast ligand rebinding in the heme domain of the oxygen sensors FixL and Dos: general regulatory implications for heme-based sensors. Proc Natl Acad Sci U S A 2002; 99:12771-6. [PMID: 12271121 PMCID: PMC130535 DOI: 10.1073/pnas.192311699] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2002] [Indexed: 11/18/2022] Open
Abstract
Heme-based oxygen sensors are part of ligand-specific two-component regulatory systems, which have both a relatively low oxygen affinity and a low oxygen-binding rate. To get insight into the dynamical aspects underlying these features and the ligand specificity of the signal transduction from the heme sensor domain, we used femtosecond spectroscopy to study ligand dynamics in the heme domains of the oxygen sensors FixL from Bradyrhizobium japonicum (FixLH) and Dos from Escherichia coli (DosH). The heme coordination with different ligands and the corresponding ground-state heme spectra of FixLH are similar to myoglobin (Mb). After photodissociation, the excited-state properties and ligand-rebinding kinetics are qualitatively similar for FixLH and Mb for CO and NO as ligands. In contrast to Mb, the transient spectra of FixLH after photodissociation of ligands are distorted compared with the ground-state difference spectra, indicating differences in the heme environment with respect to the unliganded state. This distortion is particularly marked for O(2). Strikingly, heme-O(2) recombination occurs with efficiency unprecedented for heme proteins, in approximately 5 ps for approximately 90% of the dissociated O(2). For DosH-O(2), which shows 60% sequence similarity to FixLH, but where signal detection and transmission presumably are quite different, a similarly fast recombination was found with an even higher yield. Altogether these results indicate that in these sensors the heme pocket acts as a ligand-specific trap. The general implications for the functioning of heme-based ligand sensors are discussed in the light of recent studies on heme-based NO and CO sensors.
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Affiliation(s)
- Ursula Liebl
- Laboratory for Optical Biosciences, Institut National de la Santé et de la Recherche Médicale U451, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7645, France
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32
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Youn H, Kerby RL, Thorsteinsson MV, Conrad M, Staples CR, Serate J, Beack J, Roberts GP. The heme pocket afforded by Gly117 is crucial for proper heme ligation and activity of CooA. J Biol Chem 2001; 276:41603-10. [PMID: 11551932 DOI: 10.1074/jbc.m106165200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CooA, a CO-sensing homodimeric transcription activator from Rhodospirillum rubrum, undergoes a conformational change in response to CO binding to its heme prosthetic group that allows it to bind specific DNA sequences. In a recent structural study (Lanzilotta, W. N., Schuller, D. J., Thorsteinsson, M. V., Kerby, R. L., Roberts, G. P., and Poulos, T. L. (2000) Nat. Struct. Biol. 7, 876-880), it was suggested that CO binding to CooA results in a modest repositioning of the C-helices that serve as the dimer interface. Gly(117) is one of the residues on the C-helix within 7 A of the heme iron on the Pro(2) side of the heme in CooA. Analysis of a series of Gly(117) variants revealed altered CO-sensing function and heme ligation states dependent on the size of the substituted amino acid at this position; bulky substitutions perturbed CooA both spectrally and functionally. A combination of spectroscopic and mutagenic studies showed that a representative Gly(117) variant, G117I CooA, was specifically perturbed in its Pro(2) ligation in both Fe(III) and Fe(II) forms, but comparison with other CooA variants indicated that perturbation of Pro(2) ligation is not the basis for the lack of CO response in G117I CooA. These results have led to the hypothesis that (i) the heme and the C-helix region move toward each other following CO binding and the interaction of the heme with the C-helix is crucial for CooA activation, and (ii) this event occurs only when a properly sized heme pocket is afforded.
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Affiliation(s)
- H Youn
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Thorsteinsson MV, Kerby RL, Youn H, Conrad M, Serate J, Staples CR, Roberts GP. Redox-mediated transcriptional activation in a CooA variant. J Biol Chem 2001; 276:26807-13. [PMID: 11359778 DOI: 10.1074/jbc.m102758200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CooA, the carbon monoxide-sensing transcription factor from Rhodospirillum rubrum, binds CO at a reduced (Fe(II)) heme moiety with resulting conformational changes that promote DNA binding. In this study, we report a variant of CooA, M124R, that is active in transcriptional activation in a redox-dependent manner. Where wild-type CooA is active only in the Fe(II) + CO form, M124R CooA is active in both Fe(II) + CO and Fe(III) forms. Analysis of the pH dependence of the activity of Fe(III) M124R CooA demonstrated that the activity was also coordination state-dependent with a five-coordinate, high-spin species identified as the active form and Cys(75) as the retained ligand. In contrast, the active Fe(II) + CO forms of both wild-type and M124R CooA are six-coordinate and low-spin with a protein ligand other than Cys(75), so that WT and Fe(III) M124R CooA are apparently achieving an active conformation despite two different heme coordination and ligation states. A hypothesis to explain these results is proposed. This study demonstrates the utility of CooA as a model system for the isolation of functionally interesting heme proteins.
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Affiliation(s)
- M V Thorsteinsson
- Departments of Bacteriology and Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Abstract
Most prokaryotic signal-transduction systems and a few eukaryotic pathways use phosphotransfer schemes involving two conserved components, a histidine protein kinase and a response regulator protein. The histidine protein kinase, which is regulated by environmental stimuli, autophosphorylates at a histidine residue, creating a high-energy phosphoryl group that is subsequently transferred to an aspartate residue in the response regulator protein. Phosphorylation induces a conformational change in the regulatory domain that results in activation of an associated domain that effects the response. The basic scheme is highly adaptable, and numerous variations have provided optimization within specific signaling systems. The domains of two-component proteins are modular and can be integrated into proteins and pathways in a variety of ways, but the core structures and activities are maintained. Thus detailed analyses of a relatively small number of representative proteins provide a foundation for understanding this large family of signaling proteins.
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Affiliation(s)
- A M Stock
- Center for Advanced Biotechnology and Medicine and Howard Hughes Medical Institute, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA.
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35
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Thorsteinsson MV, Kerby RL, Conrad M, Youn H, Staples CR, Lanzilotta WN, Poulos TJ, Serate J, Roberts GP. Characterization of variants altered at the N-terminal proline, a novel heme-axial ligand in CooA, the CO-sensing transcriptional activator. J Biol Chem 2000; 275:39332-8. [PMID: 11007793 DOI: 10.1074/jbc.m007691200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CooA, the carbon monoxide-sensing transcription factor from Rhodospirillum rubrum, binds CO through a heme moiety resulting in conformational changes that promote DNA binding. The crystal structure shows that the N-terminal Pro(2) of one subunit (Met(1) is removed post-translationally) provides one ligand to the heme of the other subunit in the CooA homodimer. To determine the importance of this novel ligand and the contiguous residues to CooA function, we have altered the N terminus through two approaches: site-directed mutagenesis and regional randomization, and characterized the resulting CooA variants. While Pro(2) appears to be optimal for CooA function, it is not essential and a variety of studied variants at this position have substantial CO-sensing function. Surprisingly, even alterations that add a residue (where Pro(2) is replaced by Met(1)-Tyr(2), for example) accumulate heme-containing CooA with functional properties that are similar to those of wild-type CooA. Other nearby residues, such as Phe(5) and Asn(6) appear to be important for either the structural integrity or the function of CooA. These results are contrasted with those previously reported for alteration of the His(77) ligand on the opposite side of the heme.
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Affiliation(s)
- M V Thorsteinsson
- Department of Bacteriology and the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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36
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Vogel KM, Kozlowski PM, Zgierski MZ, Spiro TG. Determinants of the FeXO (X = C, N, O) Vibrational Frequencies in Heme Adducts from Experiment and Density Functional Theory. J Am Chem Soc 1999. [DOI: 10.1021/ja990042r] [Citation(s) in RCA: 181] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kathleen M. Vogel
- Contribution from the Department of Chemistry, Princeton University, Princeton, New Jersey 08544, and Steacie Institute for Molecular Science, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
| | - Pawel M. Kozlowski
- Contribution from the Department of Chemistry, Princeton University, Princeton, New Jersey 08544, and Steacie Institute for Molecular Science, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
| | - Marek Z. Zgierski
- Contribution from the Department of Chemistry, Princeton University, Princeton, New Jersey 08544, and Steacie Institute for Molecular Science, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
| | - Thomas G. Spiro
- Contribution from the Department of Chemistry, Princeton University, Princeton, New Jersey 08544, and Steacie Institute for Molecular Science, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
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37
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Miyatake H, Mukai M, Adachi S, Nakamura H, Tamura K, Iizuka T, Shiro Y, Strange RW, Hasnain SS. Iron coordination structures of oxygen sensor FixL characterized by Fe K-edge extended x-ray absorption fine structure and resonance raman spectroscopy. J Biol Chem 1999; 274:23176-84. [PMID: 10438488 DOI: 10.1074/jbc.274.33.23176] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
FixL is a heme-based O(2) sensor protein involved in a two-component system of a symbiotic bacterium. In the present study, the iron coordination structure in the heme domain of Rhizobium meliloti FixLT (RmFixLT, a soluble truncated FixL) was examined using Fe K-edge extended x-ray absorption fine structure (EXAFS) and resonance Raman spectroscopic techniques. In the EXAFS analyses, the interatomic distances and angles of the Fe-ligand bond and the iron displacement from the heme plane were obtained for RmFixLT in the Fe(2+), Fe(2+)O(2), Fe(2+)CO, Fe(3+), Fe(3+)F(-), and Fe(3+)CN(-) states. An apparent correlation was found between the heme-nitrogen (proximal His-194) distance in the heme domain and the phosphorylation activity of the histidine kinase domain. Comparison of the Fe-CO coordination geometry between RmFixLT and RmFixLH (heme domain of RmFixL), based on the EXAFS and Raman results, has suggested that the kinase domain directly or indirectly influences steric interaction between the iron-bound ligand and the heme pocket. Referring to the crystal structure of the heme domain of Bradyrhizobium japonicum FixL (Gong, W., Hao, B., Mansy, S. S., Gonzalez, G., Gilles-Gonzalez, M. A., and Chan, M. K. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 15177-15182), we discussed details of the iron coordination structure of RmFixLT and RmFixLH in relation to an intramolecular signal transduction mechanism in its O(2) sensing.
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Affiliation(s)
- H Miyatake
- Institute of Physical and Chemical Research, RIKEN Harima Institute, Mikazuki-cho, Sayo, Hyogo 679-5143, Japan
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38
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Watmough NJ, Butland G, Cheesman MR, Moir JW, Richardson DJ, Spiro S. Nitric oxide in bacteria: synthesis and consumption. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1411:456-74. [PMID: 10320675 DOI: 10.1016/s0005-2728(99)00032-8] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- N J Watmough
- School of Biological Sciences, Centre for Metalloprotein Spectroscopy and Biology, University of East Anglia, Norwich NR4 7TJ, UK.
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Abstract
The past several years have been witness to a staggering rate of advancement in the understanding of how organisms respond to changes in the availability of diatomic molecules that are toxic and/or crucial to survival. Heme-based sensors presently constitute the majority of the proteins known to sense NO, O2 and CO and to initiate the chemistry required to adapt to changes in their availabilities. Knowledge of the three characterized members of this class, soluble guanylate cyclase, FixL and CooA, has grown substantially during the past year. The major advances have resulted from a broad range of approaches to elucidation of both function and mechanism. They include growth in the understanding of the interplay between the heme and protein in soluble guanylate cyclase, as well as alternate means for its stimulation. Insight into the O2-induced structural changes in FixL has been supplied by the single crystal structure of the heme domain of Bradyrhizobium japonicum. Finally, the ligation environment and ligand interchange that facilitates CO sensing by CooA has been established by spectroscopic and mutagenesis techniques.
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Affiliation(s)
- K R Rodgers
- Department of Chemistry, Ladd Hall, North Dakota State University, Fargo, ND 58105-5516, USA
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Zhu H, Bunn HF. Oxygen sensing and signaling: impact on the regulation of physiologically important genes. RESPIRATION PHYSIOLOGY 1999; 115:239-47. [PMID: 10385037 PMCID: PMC3045521 DOI: 10.1016/s0034-5687(99)00024-9] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A growing number of physiologically relevant genes are regulated in response to changes in intracellular oxygen tension. It is likely that cells from a wide variety of tissues share a common mechanism of oxygen sensing and signal transduction leading to the activation of the transcription factor hypoxia-inducible factor 1 (HIF-1). Besides hypoxia, transition metals (Co2+, Ni2+ and Mn2+) and iron chelation also promote activation of HIF-1. Induction of HIF-1 by hypoxia is blocked by the heme ligands carbon monoxide and nitric oxide. There is growing, albeit indirect, evidence that the oxygen sensor is a flavoheme protein and that the signal transduction pathway involves changes in the level of intracellular reactive oxygen intermediates. The activation of HIF-1 by hypoxia depends upon signaling-dependent rescue of its alpha-subunit from oxygen-dependent degradation in the proteasome, allowing it to form a heterodimer with HIF-1beta (ARNT), which then translocates to the nucleus and impacts on the transcription of genes whose cis-acting elements contain cognate hypoxia response elements.
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Affiliation(s)
| | - H. Franklin Bunn
- Corresponding author. Tel.: +1-617-7325841; fax: +1-617-7390748. (H.F. Bunn)
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41
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Goudreau PN, Stock AM. Signal transduction in bacteria: molecular mechanisms of stimulus-response coupling. Curr Opin Microbiol 1998; 1:160-9. [PMID: 10066483 DOI: 10.1016/s1369-5274(98)80006-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In bacteria, adaptive responses to changing environmental conditions are mediated by signal transduction systems that involve modular protein domains. Despite great diversity in the integration of domains into different systems, studies of individual components have revealed molecular strategies that are widely applicable. Studies of receptors have advanced our understanding of how information is transmitted across membranes, the determination of three-dimensional structures of domains of histidine protein kinase domains and response regulator proteins has begun to reveal the molecular basis of signaling via two-component phosphoryltransfer pathways, and the description of 'eukaryotic-like' protein domains involved in bacterial signaling has emphasized the universality of intracellular signaling mechanisms.
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Affiliation(s)
- P N Goudreau
- Center for Advanced Biotechnology and Medicine, Howard Hughes Medical Institute, University of Medicine and Dentistry of New Jersey, 679 HoesLane, Piscataway, NJ 08854-5638, USA.
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