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Ibrahim IM, Wu H, Ezhov R, Kayanja GE, Zakharov SD, Du Y, Tao WA, Pushkar Y, Cramer WA, Puthiyaveetil S. An evolutionarily conserved iron-sulfur cluster underlies redox sensory function of the Chloroplast Sensor Kinase. Commun Biol 2020; 3:13. [PMID: 31925322 PMCID: PMC6949291 DOI: 10.1038/s42003-019-0728-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 12/08/2019] [Indexed: 11/09/2022] Open
Abstract
Photosynthetic efficiency depends on equal light energy conversion by two spectrally distinct, serially-connected photosystems. The redox state of the plastoquinone pool, located between the two photosystems, is a key regulatory signal that initiates acclimatory changes in the relative abundance of photosystems. The Chloroplast Sensor Kinase (CSK) links the plastoquinone redox signal with photosystem gene expression but the mechanism by which it monitors the plastoquinone redox state is unclear. Here we show that the purified Arabidopsis and Phaeodactylum CSK and the cyanobacterial CSK homologue, Histidine kinase 2 (Hik2), are iron-sulfur proteins. The Fe-S cluster of CSK is further revealed to be a high potential redox-responsive [3Fe-4S] center. CSK responds to redox agents with reduced plastoquinone suppressing its autokinase activity. Redox changes within the CSK iron-sulfur cluster translate into conformational changes in the protein fold. These results provide key insights into redox signal perception and propagation by the CSK-based chloroplast two-component system.
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Affiliation(s)
- Iskander M Ibrahim
- Department of Biochemistry and Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Huan Wu
- Department of Biochemistry and Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Roman Ezhov
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Avenue, West Lafayette, IN, 47907, USA
| | - Gilbert E Kayanja
- Department of Biochemistry and Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Stanislav D Zakharov
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Yanyan Du
- Department of Biochemistry and Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA.,Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Weiguo Andy Tao
- Department of Biochemistry and Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Yulia Pushkar
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Avenue, West Lafayette, IN, 47907, USA
| | - William A Cramer
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Sujith Puthiyaveetil
- Department of Biochemistry and Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA.
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Kuchenreuther JM, Britt RD, Swartz JR. New insights into [FeFe] hydrogenase activation and maturase function. PLoS One 2012; 7:e45850. [PMID: 23049878 PMCID: PMC3457958 DOI: 10.1371/journal.pone.0045850] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 08/23/2012] [Indexed: 11/18/2022] Open
Abstract
[FeFe] hydrogenases catalyze H(2) production using the H-cluster, an iron-sulfur cofactor that contains carbon monoxide (CO), cyanide (CN(-)), and a dithiolate bridging ligand. The HydE, HydF, and HydG maturases assist in assembling the H-cluster and maturing hydrogenases into their catalytically active form. Characterization of these maturases and in vitro hydrogenase activation methods have helped elucidate steps in the H-cluster biosynthetic pathway such as the HydG-catalyzed generation of the CO and CN(-) ligands from free tyrosine. We have refined our cell-free approach for H-cluster synthesis and hydrogenase maturation by using separately expressed and purified HydE, HydF, and HydG. In this report, we illustrate how substrates and protein constituents influence hydrogenase activation, and for the first time, we show that each maturase can function catalytically during the maturation process. With precise control over the biomolecular components, we also provide evidence for H-cluster synthesis in the absence of either HydE or HydF, and we further show that hydrogenase activation can occur without exogenous tyrosine. Given these findings, we suggest a new reaction sequence for the [FeFe] hydrogenase maturation pathway. In our model, HydG independently synthesizes an iron-based compound with CO and CN(-) ligands that is a precursor to the H-cluster [2Fe](H) subunit, and which we have termed HydG-co. We further propose that HydF is a transferase that stabilizes HydG-co and also shuttles the complete [2Fe](H) subcluster to the hydrogenase, a translocation process that may be catalyzed by HydE. In summary, this report describes the first example of reconstructing the [FeFe] hydrogenase maturation pathway using purified maturases and subsequently utilizing this in vitro system to better understand the roles of HydE, HydF, and HydG.
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Affiliation(s)
- Jon M Kuchenreuther
- Department of Chemical Engineering, Stanford University, Stanford, California, USA
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Soboh B, Igarashi RY, Hernandez JA, Rubio LM. Purification of a NifEN protein complex that contains bound molybdenum and a FeMo-Co precursor from an Azotobacter vinelandii DeltanifHDK strain. J Biol Chem 2006; 281:36701-9. [PMID: 17012743 DOI: 10.1074/jbc.m606820200] [Citation(s) in RCA: 18] [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
The NifEN protein complex serves as a molecular scaffold where some of the steps for the assembly of the iron-molybdenum cofactor (FeMo-co) of nitrogenase take place. A His-tagged version of the NifEN complex has been previously purified and shown to carry two identical [4Fe-4S] clusters of unknown function and a [Fe-S]-containing FeMo-co precursor. We have improved the purification of the his-NifEN protein from a DeltanifHDK strain of Azotobacter vinelandii and have found that the amounts of iron and molybdenum within NifEN were significantly higher than those reported previously. In an in vitro FeMo-co synthesis system with purified components, the NifEN protein served as a source of both molybdenum and a [Fe-S]-containing FeMo-co precursor, showing significant FeMo-co synthesis activity in the absence of externally added molybdate. Thus, the NifEN scaffold protein, purified from DeltanifHDK background, contained the Nif-Bco-derived Fe-S cluster and molybdenum, although these FeMo-co constituents were present at different levels within the protein complex.
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Affiliation(s)
- Basem Soboh
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California 94720, USA
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5
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Agarwalla S, Stroud RM, Gaffney BJ. Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA: optical and EPR studies. J Biol Chem 2004; 279:34123-9. [PMID: 15181002 PMCID: PMC1237038 DOI: 10.1074/jbc.m405702200] [Citation(s) in RCA: 29] [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
An unprecedented [4Fe-4S] iron-sulfur cluster was found in RumA, the enzyme that methylates U1939 in Escherichia coli 23 S ribosomal RNA (Agarwalla, S., Kealey, J. T., Santi, D. V., and Stroud, R. M. (2002) J. Biol. Chem. 277, 8835-8840; Lee, T. T., Agarwalla, S., and Stroud, R. M. (2004) Structure 12, 397-407). Methyltransferase reactions do not involve a redox step. To understand the structural and functional roles of the cluster in RumA, we have characterized redox reactions of the iron-sulfur cluster. As isolated aerobically, RumA exhibits a visible absorbance maximum at 390 nm and is EPR silent. It cannot be reduced by anaerobic additions of dithionite. Photoreduction by deazariboflavin/EDTA gives EPR spectra, the quantity (56% of S = 1/2 species) and details (g(av) approximately 1.96-1.93) of which indicate a [4Fe-4S](1+) cluster in the reduced RumA. Oxidation of RumA by ferricyanide leads to loss of the 390-nm band and appearance of lower intensity bands at 444 and 520 nm. EPR spectra of ferricyanide-oxidized RumA show a fraction (<8%) of the FeS cluster trapped in the [3Fe-4S](1+) form (g(av) approximately 2.011) together with unusual radical-like spectrum (g' values 2.015, 2.00, and 1.95). RumA also reacts with nitric oxide to give EPR spectra characteristic of the protein-bound iron dinitrosyl species. Oxidation of the cluster leads to its decomposition and that could be a mechanism for regulating the activity of RumA under conditions of oxidative stress in the cell. Sequence data base searches revealed that RumA homologs are widespread in various kingdoms of life and contain a conserved and unique iron-sulfur cluster binding motif, CX(5)CGGC.
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Affiliation(s)
- Sanjay Agarwalla
- From the Department of Biochemistry and Biophysics, University of California, San Francisco, California 94107 and the
- § To whom correspondence may be addressed: Dept. of Biochemistry and Biophysics, University of California, San Francisco, CA 94107. Tel.: 415-476-3937; Fax: 415-476-1902; E-mail:
| | - Robert M. Stroud
- From the Department of Biochemistry and Biophysics, University of California, San Francisco, California 94107 and the
| | - Betty J. Gaffney
- Biological Sciences Department, Florida State University, Tallahassee, Florida 32306
- || To whom correspondence may be addressed: Biological Sciences Department, Florida State University, Tallahassee, FL 32306. Tel.: 850-644-8547; E-mail:
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Morgan T, Prince RC, Mortenson LE. Electrochemical titration of theS= 3/2 andS= ½ states of the iron protein of nitrogenase. FEBS Lett 2001. [DOI: 10.1016/0014-5793(86)81329-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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Stephens P, Devlin F, McKenna M, Morgan T, Czechowski M, DerVartanian D, Peck H, LeGall J. Magnetic circular dichroism of DCPIP-oxidised Desulfovibrio vulgaris
hydrogenase. FEBS Lett 2001. [DOI: 10.1016/0014-5793(85)80223-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Direct electrochemistry in the characterisation of redox proteins: Novel properties of Azotobacter
7Fe ferredoxin. FEBS Lett 2001. [DOI: 10.1016/0014-5793(88)81313-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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9
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Jung YS, Bonagura CA, Tilley GJ, Gao-Sheridan HS, Armstrong FA, Stout CD, Burgess BK. Structure of C42D Azotobacter vinelandii FdI. A Cys-X-X-Asp-X-X-Cys motif ligates an air-stable [4Fe-4S]2+/+ cluster. J Biol Chem 2000; 275:36974-83. [PMID: 10961993 DOI: 10.1074/jbc.m004947200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
All naturally occurring ferredoxins that have Cys-X-X-Asp-X-X-Cys motifs contain [4Fe-4S](2+/+) clusters that can be easily and reversibly converted to [3Fe-4S](+/0) clusters. In contrast, ferredoxins with unmodified Cys-X-X-Cys-X-X-Cys motifs assemble [4Fe-4S](2+/+) clusters that cannot be easily interconverted with [3Fe-4S](+/0) clusters. In this study we changed the central cysteine of the Cys(39)-X-X-Cys(42)-X-X-Cys(45) of Azotobacter vinelandii FdI, which coordinates its [4Fe-4S](2+/+) cluster, into an aspartate. UV-visible, EPR, and CD spectroscopies, metal analysis, and x-ray crystallography show that, like native FdI, aerobically purified C42D FdI is a seven-iron protein retaining its [4Fe-4S](2+/+) cluster with monodentate aspartate ligation to one iron. Unlike known clusters of this type the reduced [4Fe-4S](+) cluster of C42D FdI exhibits only an S = 1/2 EPR with no higher spin signals detected. The cluster shows only a minor change in reduction potential relative to the native protein. All attempts to convert the cluster to a 3Fe cluster using conventional methods of oxygen or ferricyanide oxidation or thiol exchange were not successful. The cluster conversion was ultimately accomplished using a new electrochemical method. Hydrophobic and electrostatic interaction and the lack of Gly residues adjacent to the Asp ligand explain the remarkable stability of this cluster.
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Affiliation(s)
- Y S Jung
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
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10
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Iwasaki T, Watanabe E, Ohmori D, Imai T, Urushiyama A, Akiyama M, Hayashi-Iwasaki Y, Cosper NJ, Scott RA. Spectroscopic investigation of selective cluster conversion of archaeal zinc-containing ferredoxin from Sulfolobus sp. strain 7. J Biol Chem 2000; 275:25391-401. [PMID: 10827091 DOI: 10.1074/jbc.m909243199] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Archaeal zinc-containing ferredoxin from Sulfolobus sp. strain 7 contains one [3Fe-4S] cluster (cluster I), one [4Fe-4S] cluster (cluster II), and one isolated zinc center. Oxidative degradation of this ferredoxin led to the formation of a stable intermediate with 1 zinc and approximately 6 iron atoms. The metal centers of this intermediate were analyzed by electron paramagnetic resonance (EPR), low temperature resonance Raman, x-ray absorption, and (1)H NMR spectroscopies. The spectroscopic data suggest that (i) cluster II was selectively converted to a cubane [3Fe-4S](1+) cluster in the intermediate, without forming a stable radical species, and that (ii) the local metric environments of cluster I and the isolated zinc site did not change significantly in the intermediate. It is concluded that the initial step of oxidative degradation of the archaeal zinc-containing ferredoxin is selective conversion of cluster II, generating a novel intermediate containing two [3Fe-4S] clusters and an isolated zinc center. At this stage, significant structural rearrangement of the protein does not occur. We propose a new scheme for oxidative degradation of dicluster ferredoxins in which each cluster converts in a stepwise manner, prior to apoprotein formation, and discuss its structural and evolutionary implications.
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Affiliation(s)
- T Iwasaki
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Sendagi, Tokyo, Japan. iwasaki/
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11
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Sticht H, Rösch P. The structure of iron-sulfur proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1998; 70:95-136. [PMID: 9785959 DOI: 10.1016/s0079-6107(98)00027-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ferredoxins are a group of iron-sulfur proteins for which a wealth of structural and mutational data have recently become available. Previously unknown structures of ferredoxins which are adapted to halophilic, acidophilic or hyperthermophilic environments and new cysteine patterns for cluster ligation and non-cysteine cluster ligation have been described. Site-directed mutagenesis experiments have given insight into factors that influence the geometry, stability, redox potential, electronic properties and electron-transfer reactivity of iron-sulfur clusters.
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Affiliation(s)
- H Sticht
- Lehrstuhl für Struktur und Chemie der Biopolymere, Universität Bayreuth, Germany.
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12
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Iwasaki T, Oshima T. A stable intermediate product of the archaeal zinc-containing 7Fe ferredoxin from Sulfolobus sp. strain 7 by artificial oxidative conversion. FEBS Lett 1997; 417:223-6. [PMID: 9395300 DOI: 10.1016/s0014-5793(97)01286-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Irreversible conversion of the purified zinc-containing 7Fe ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7 was found to occur under aerobic conditions at pH 5.0 and at 4 degrees C. This process accompanied a substantial increase of the electron paramagnetic resonance signal attributed to a [3Fe-4S]1+ cluster, and the converted form containing approximately 6 Fe/Zn (mol/mol) had a net charge different from that of the native 7Fe ferredoxin. These data provide evidence for the formation of a stable intermediate product of the archaeal ferredoxin having two [3Fe-4S] clusters and a zinc center by artificial oxidative degradation. This further explains the discrepancy that a zinc center and two [3Fe-4S] clusters (but not a zinc center and one [3Fe-4S] cluster plus one [4Fe-4S] cluster) are observed in the crystal structure at pH 5.0.
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Affiliation(s)
- T Iwasaki
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
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13
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Bian S, Hemann CF, Hille R, Cowan JA. Characterization of an autoreduction pathway for the [Fe4S4]3+ cluster of mutant Chromatium vinosum high-potential iron proteins. Site-directed mutagenesis studies to probe the role of phenylalanine 66 in defining the stability of the [Fe4S4] center provide evidence for oxidative degradation via a [Fe3S4] cluster. Biochemistry 1996; 35:14544-52. [PMID: 8931551 DOI: 10.1021/bi961658l] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A number of point mutations of the conserved aromatic residue phenylalanine 66 (Phe66Tyr, -Asn, -Cys, -Ser) in Chromatium vinosum high-potential iron sulfur protein have been examined with the aim of understanding the functional role of this residue. Nonconservative replacements with polar residues have a minimal effect on the midpoint potential of the [Fe4S4]3+/2+ cluster, typically < +25 mV, with a maximum change of +40 mV for Phe66Asn. With the exception of the Phe66Tyr mutant, the oxidized state was found to be unstable relative to the recombinant native, with regeneration of the reduced state. The pathway for this transformation involves degradation of the cluster in a fraction of the sample, which provides the reducing equivalents required to bring about reduction of the remainder of the sample. This degradative reaction proceeds through a transient [Fe3S4]+ intermediate that is characterized by typical g values and power saturation behavior and is prompted by the increased solvent accessibility of the cluster core in the nonconservative Phe66 mutants as evidenced by 1H-15N HMQC NMR experiments. These results are consistent with a model where the critical role of the aromatic residues in the high-potential iron proteins is to protect the cluster from hydrolytic degradation in the oxidized state.
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Affiliation(s)
- S Bian
- Evans Laboratory of Chemistry, Ohio State University, Columbus 43210, USA
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14
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Imai T, Kamata K, Saito H, Urushiyama A. Effect of Hexacyanoferrate(III) onMycobacterium smegmatis7Fe Ferredoxin: Further Evidence for Formation of a 6Fe(2 × [3Fe–4S]) Ferredoxin. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1995. [DOI: 10.1246/bcsj.68.2923] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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15
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Hu Z, Jollie D, Burgess BK, Stephens PJ, Münck E. Mössbauer and EPR studies of Azotobacter vinelandii ferredoxin I. Biochemistry 1994; 33:14475-85. [PMID: 7981208 DOI: 10.1021/bi00252a014] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Azotobacter vinelandii ferredoxin I (FdI) is a small protein that contains one Fe4S4 cluster and one Fe3S4 cluster. Previous studies of FdI have shown that the redox potential of the Fe3S4 cluster and the MCD and CD spectra of the reduced Fe3S4 cluster are pH-dependent. Using Mössbauer and EPR spectroscopy, we have studied FdI in different oxidation states and at different pH values. Here, we report the spin Hamiltonian parameters of the oxidized (S = 1/2) Fe3S4 cluster at pH 7.4 and the reduced (S = 2) Fe3S4 cluster at pH 6.0 and 8.5. The pH dependence observed by MCD is also evident in the Mössbauer spectra which show a change of the magnetic hyperfine tensor for one Fe site of the valence-delocalized pair. The Fe4S4 cluster is ligated by cysteines 20, 39, 42, and 45, but not by the adjacent cysteine 24. Treatment of FdI with 3 equiv of ferricyanide alters the Fe4S4 cluster, yielding a new species, [Fe4S4]'. The S = 1/2 EPR signal of [Fe4S4]' has previously been attributed to the formation of a cysteine disulfide radical from Cys24 and cluster sulfide. Here we show that the EPR signal is broadened by 57Fe, indicating that the electronic spin is significantly coupled to the cluster iron. Consistent with this, substantial magnetic hyperfine interactions are observed by Mössbauer spectroscopy. In addition, the average isomer shift of the four Fe sites is smaller for [Fe4S4]' than for [Fe4S4]2+, indicating that the oxidation is iron-based to at least some extent. Incubation of FdI with excess ferricyanide destroys the Fe4S4 cluster but leaves the Fe3S4 cluster intact. Our studies of (3Fe)FdI show that the S = 1/2 spin of the Fe3S4 cluster interacts with another paramagnet, presumably a radical generated at the site left vacant by the removal of the Fe4S4 cluster.
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Affiliation(s)
- Z Hu
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213-3890
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16
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Shen B, Jollie D, Stout C, Diller T, Armstrong F, Gorst C, La Mar G, Stephens P, Burgess B. Azotobacter vinelandii ferredoxin I. Alteration of individual surface charges and the [4FE-4S]2+/+ cluster reduction potential. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)37232-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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17
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18
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Armstrong FA. Dynamic Electrochemistry of Iron—Sulfur Proteins. ADVANCES IN INORGANIC CHEMISTRY 1992. [DOI: 10.1016/s0898-8838(08)60063-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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19
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Site-directed mutagenesis of Azotobacter vinelandii ferredoxin I. Changes in [4Fe-4S] cluster reduction potential and reactivity. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)54675-5] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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20
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Stephens PJ, Jensen GM, Devlin FJ, Morgan TV, Stout CD, Martin AE, Burgess BK. Circular dichroism and magnetic circular dichroism of Azotobacter vinelandii ferredoxin I. Biochemistry 1991; 30:3200-9. [PMID: 2009261 DOI: 10.1021/bi00227a007] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Room temperature circular dichroism (CD) and low temperature magnetic circular dichroism (MCD) spectra of air-oxidized and dithionite-reduced Azotobacter vinelandii ferredoxin I (FdI), a [( 4Fe-4S]2+/1+, [3Fe-4S]1+/0) protein, are reported. Unlike the CD of oxidized FdI, the CD of dithionite-reduced FdI exhibits significant pH dependence, consistent with protonation-deprotonation at or near the cluster reduced: the [3Fe-4S] cluster. The MCD of reduced FdI, which originates in the paramagnetic reduced [3Fe-4S]0 cluster, is also pH-dependent. Detailed studies of the field dependence and temperature dependence of the MCD of oxidized and reduced FdI, in the latter case at pH 6.0 and 8.3, are reported. The low-field temperature dependence of the MCD of oxidized FdI, which originates in the paramagnetic oxidized [3Fe-4S]1+ cluster, establishes the absence of a significant population of excited electronic states of this cluster up to 60 K. The low-field temperature dependence of the MCD of reduced FdI establishes that the ground-state manifold of the reduced [3Fe-4S]0 cluster possesses S greater than or equal to 2 at both pH 6.0 and 8.3. Analysis, assuming S = 2 and an axial zero-field splitting Hamiltonian, leads to D = -2.0 and -3.5 cm-1 at pH 6.0 and 8.3, respectively. The site of the (de)protonation affecting the spectroscopic properties of the [3Fe-4S] cluster remains unknown.
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Affiliation(s)
- P J Stephens
- Department of Chemistry, University of Southern California, Los Angeles 90089-0482
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21
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Martín AE, Burgess BK, Stout CD, Cash VL, Dean DR, Jensen GM, Stephens PJ. Site-directed mutagenesis of Azotobacter vinelandii ferredoxin I: [Fe-S] cluster-driven protein rearrangement. Proc Natl Acad Sci U S A 1990; 87:598-602. [PMID: 2153958 PMCID: PMC53312 DOI: 10.1073/pnas.87.2.598] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Azotobacter vinelandii ferredoxin I is a small protein that contains one [4Fe-4S] cluster and one [3Fe-4S] cluster. Recently the x-ray crystal structure has been redetermined and the fdxA gene, which encodes the protein, has been cloned and sequenced. Here we report the site-directed mutation of Cys-20, which is a ligand of the [4Fe-4S] cluster in the native protein, to alanine and the characterization of the protein product by x-ray crystallographic and spectroscopic methods. The data show that the mutant protein again contains one [4Fe-4S] cluster and one [3Fe-4S] cluster. The new [4Fe-4S] cluster obtains its fourth ligand from Cys-24, a free cysteine in the native structure. The formation of this [4Fe-4S] cluster drives rearrangement of the protein structure.
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Affiliation(s)
- A E Martín
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717
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22
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Martin AE, Burgess BK, Iismaa SE, Smartt CT, Jacobson MR, Dean DR. Construction and characterization of an Azotobacter vinelandii strain with mutations in the genes encoding flavodoxin and ferredoxin I. J Bacteriol 1989; 171:3162-7. [PMID: 2722744 PMCID: PMC210031 DOI: 10.1128/jb.171.6.3162-3167.1989] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Flavodoxin and ferredoxin I have both been implicated as components of the electron transport chain to nitrogenase in the aerobic bacterium Azotobacter vinelandii. Recently, the genes encoding flavodoxin (nifF) and ferredoxin I (fdxA) were cloned and sequenced and mutants were constructed which are unable to synthesize either flavodoxin (DJ130) or ferredoxin I (LM100). Both single mutants grow at wild-type rates under N2-fixing conditions. Here we report the construction of a double mutant (DJ138) which does not synthesize either flavodoxin or ferredoxin I. When plated on ammonium-containing medium, this mutant had a very small colony size when compared with the wild type, and in liquid culture with ammonium, this double mutant grew three times slower than the wild type or single mutant strains. This demonstrated that there is an important metabolic function unrelated to nitrogen fixation that is normally carried out by either flavodoxin or ferredoxin. If either one of these proteins is missing, the other can substitute for it. The double mutant phenotype can now be used to screen site-directed mutant versions of ferredoxin I for functionality in vivo even though the specific function of ferredoxin I is still unknown. The double mutant grew at the same slow rate under N2-fixing conditions. Thus, A. vinelandii continues to fix N2 even when both flavodoxin and ferredoxin I are missing, which suggests that a third as yet unidentified protein also serves as an electron donor to nitrogenase.
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Affiliation(s)
- A E Martin
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717
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M. Lough S, B. Jacobs D, F. Parker S, W. Mcdonald J, D. Watt G. A facile method of isolation for the iron molybdenum cofactor of nitrogenase and bacterial ferritin from extracts of azotobacter vinelandii. Inorganica Chim Acta 1988. [DOI: 10.1016/s0020-1693(00)83471-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Stout GH, Turley S, Sieker LC, Jensen LH. Structure of ferredoxin I from Azotobacter vinelandii. Proc Natl Acad Sci U S A 1988; 85:1020-2. [PMID: 3422475 PMCID: PMC279692 DOI: 10.1073/pnas.85.4.1020] [Citation(s) in RCA: 99] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The structure of Azotobacter vinelandii ferredoxin I (Av FdI, 106 amino acids) has been redetermined, based on x-ray diffraction data from tetragonal crystals of the native protein and two heavy atom derivatives. The current model differs greatly from the one previously reported and is in agreement with arguments based on various spectroscopic and other methods. The unit cell parameters are a = b = 55.62 A and c = 95.51 A, whereas the space group was found to be P4(1)2(1)2 instead of P4(3)2(1)2. The sequence of the first half of Av FdI is closely homologous with ferredoxin from Peptococcus aerogenes (Pa Fd, 54 amino acids) and the fold of the corresponding chain is almost identical. The ligands of the 3Fe complex are Cys-8, -16, and -49, corresponding to three of the four ligands in complex I of Pa Fd; the ligands of the 4Fe complex are Cys-20, -39, -42, and -45, corresponding to the four ligands in complex II of Pa Fd.
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Affiliation(s)
- G H Stout
- Department of Biological Structure, University of Washington School of Medicine 98195
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Telser J, Benecky MJ, Adams MW, Mortenson LE, Hoffman BM. An EPR and electron nuclear double resonance investigation of carbon monoxide binding to hydrogenase I (bidirectional) from Clostridium pasteurianum W5. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)67051-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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[4Fe-4S]-cluster-depleted Azotobacter vinelandii ferredoxin I: a new 3Fe iron-sulfur protein. Proc Natl Acad Sci U S A 1985; 82:5661-5. [PMID: 2994040 PMCID: PMC390611 DOI: 10.1073/pnas.82.17.5661] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Fe(CN)6(-3) oxidation of the aerobically isolated 7Fe Azotobacter vinelandii ferredoxin I, (7Fe)FdI, is a degradative reaction. Destruction of the [4Fe-4S] cluster occurs first, followed by destruction of the [3Fe-3S] cluster. At a Fe(CN)6(-3)/(7Fe)FdI concentration ratio of 20, the product is a mixture of apoprotein and protein containing only a [3Fe-3S] cluster, (3Fe)FdI. This protein mixture, after partial purification, has been characterized by absorption, CD, magnetic CD, and EPR and Fe x-ray absorption spectroscopies. EPR and magnetic CD spectra provide strong evidence that the [3Fe-3S] cluster in (3Fe)FdI is essentially identical in structure to that in (7Fe)FdI. Analysis of the extended x-ray absorption fine structure (EXAFS) of (3Fe)FdI finds Fe scattering at an average Fe...Fe distance of approximately equal to 2.7 A. The structure of the oxidized [3Fe-3S] cluster in solutions of oxidized (3Fe)FdI, and, by extension, of oxidized (7Fe)FdI, is thus different from that obtained by x-ray crystallography on oxidized (7Fe)FdI. Possible interpretations of this result are discussed.
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Morgan TV, Stephens PJ, Devlin F, Burgess BK, Stout CD. Selective oxidative destruction of iron-sulfur clusters. Ferricyanide oxidation of Azotobacter vinelandii ferredoxin I. FEBS Lett 1985; 183:206-10. [PMID: 2985428 DOI: 10.1016/0014-5793(85)80777-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The destructive oxidation of aerobically isolated 7Fe Azotobacter vinelandii ferredoxin I [(7Fe)FdI] by Fe(CN)3-6 is examined using low-temperature magnetic circular dichroism (MCD) and EPR. The results demonstrate that oxidation of the [3Fe-3S] cluster occurs only after essentially complete destruction of the [4Fe-4S] cluster. It is therefore feasible by controlled Fe(CN)3-6 oxidation to obtain a partially metallated form of FdI, (3Fe)FdI, containing only a [3Fe-3S] cluster. The MCD and EPR data demonstrate that the [3Fe-3S] cluster in (3Fe)FdI is essentially identical in structure to that in the native protein.
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A study of one of the iron-sulphur clusters in oxidized hydrogenase from Megasphaera elsdenii by magnetic-circular-dichroism spectroscopy. Biochem J 1985; 227:333-6. [PMID: 2986607 PMCID: PMC1144844 DOI: 10.1042/bj2270333] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The m.c.d. spectrum of the oxidized state of hydrogenase from Megasphaera elsdenii has been measured at liquid-helium temperatures. This oxidation state of the enzyme displays a characteristic rhombic e.p.r. signal with g-values of 2.101, 2.052 and 2.005 assigned previously to a [4Fe-4S]3+ cluster as in oxidized HiPIP (high-potential iron-sulphur protein) [Van Dijk, Grande, Mayhew & Veeger (1980) Eur. J. Biochem. 107, 251-261]. The low-temperature m.c.d. spectrum shows no features attributable to an oxidized four-iron cluster of the HiPIP type, but does reveal broad, positive peaks at 460 and 730 nm, which magnetize in a manner untypical of a spin S = 1/2 cluster with g-values close to 2. The m.c.d. spectrum is most closely similar to that of dye-oxidized P-clusters known in the enzyme nitrogenase. It is therefore proposed that the rhombic e.p.r. spectrum at a g-value close to 2 arises from an m.c.d.-silent radical species that may be related chemically to the cysteine persulphide species, RS-S., recently found in the hexacyanoferrate-oxidized seven-iron ferredoxin of Azotobacter vinelandii [Morgan, Stephens, Devlin, Stout, Melis & Burgess (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 1931-1935].
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Wang ZC, Burns A, Watt GD. Complex formation and O2 sensitivity of Azotobacter vinelandii nitrogenase and its component proteins. Biochemistry 1985; 24:214-21. [PMID: 2986674 DOI: 10.1021/bi00322a031] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The O2 stability of the MoFe protein, the Fe protein, a 1:1 mixture of these proteins, and a 1:1 mixture in the presence of the Azotobacter vinelandii FeS-II protein has been studied as a function of time under controlled O2 partial pressures. The Fe protein is much more sensitive to O2 exposure than is the MoFe protein. The presence of the FeS-II protein at a 1:1 ratio with the component proteins measurably increases the O2 stability of the MoFe and Fe proteins. O2 inactivation of the MoFe protein was studied in some detail and found to be quite complex. At least three partially overlapping reactions are suggested. The first is the reversible oxidation of the metal clusters of the MoFe protein to the combined extent of 12 electrons with full retention of activity. The second phase consists primarily of activity loss with little increase in the extent of reversible oxidation. The third phase continues to decrease the protein activity but is also accompanied by formation of a g = 2.0 EPR signal and more extensive oxidation. Ultracentrifugation studies of the FeS-II protein at a 1:1:1 ratio with the Fe and MoFe proteins do not support the formation of the Bulen complex. The formation of other O2-stable complexes is discussed.
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Wang G, Benecky MJ, Huynh BH, Cline JF, Adams MW, Mortenson LE, Hoffman BM, Münck E. Mössbauer and electron nuclear double resonance study of oxidized bidirectional hydrogenase from Clostridium pasteurianum W5. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)42596-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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George SJ, Richards AJ, Thomson AJ, Yates MG. Azotobacter chroococcum 7Fe ferredoxin. Two pH-dependent forms of the reduced 3Fe clusters and its conversion to a 4Fe cluster. Biochem J 1984; 224:247-51. [PMID: 6095817 PMCID: PMC1144420 DOI: 10.1042/bj2240247] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Ferredoxin from Azotobacter chroococcum has been studied by low-temperature magnetic-circular-dichroism and electron-paramagnetic-resonance spectroscopy. When aerobically isolated ferredoxin contains a [3Fe-4S] and [4Fe-4S] cluster. Anaerobic treatment with dithionite in the presence of ethanediol reduces the [3Fe-4S] cluster to give two spectroscopically distinct forms RI and RII which are reversibly interconvertible with a pKa approximately 7.5. The higher-pH form, RII, has a high affinity for ferrous ion and converts readily to a [4Fe-4S]1+ cluster, scavenging iron from the medium. The presence of the iron chelator EDTA inhibits this conversion.
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