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Hough MA, Andrew CR. Cytochromes c': Structure, Reactivity and Relevance to Haem-Based Gas Sensing. Adv Microb Physiol 2015; 67:1-84. [PMID: 26616515 DOI: 10.1016/bs.ampbs.2015.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cytochromes c' are a group of class IIa cytochromes with pentacoordinate haem centres and are found in photosynthetic, denitrifying and methanotrophic bacteria. Their function remains unclear, although roles in nitric oxide (NO) trafficking during denitrification or in cellular defence against nitrosoative stress have been proposed. Cytochromes c' are typically dimeric with each c-type haem-containing monomer folding as a four-α-helix bundle. Their hydrophobic and crowded distal sites impose severe restrictions on the binding of distal ligands, including diatomic gases. By contrast, NO binds to the proximal haem face in a similar manner to that of the eukaryotic NO sensor, soluble guanylate cyclase and bacterial analogues. In this review, we focus on how structural features of cytochromes c' influence haem spectroscopy and reactivity with NO, CO and O2. We also discuss the relevance of cytochrome c' to understanding the mechanisms of gas binding to haem-based sensor proteins.
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Tsai AL, Martin E, Berka V, Olson JS. How do heme-protein sensors exclude oxygen? Lessons learned from cytochrome c', Nostoc puntiforme heme nitric oxide/oxygen-binding domain, and soluble guanylyl cyclase. Antioxid Redox Signal 2012; 17:1246-63. [PMID: 22356101 PMCID: PMC3430480 DOI: 10.1089/ars.2012.4564] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
SIGNIFICANCE Ligand selectivity for dioxygen (O(2)), carbon monoxide (CO), and nitric oxide (NO) is critical for signal transduction and is tailored specifically for each heme-protein sensor. Key NO sensors, such as soluble guanylyl cyclase (sGC), specifically recognized low levels of NO and achieve a total O(2) exclusion. Several mechanisms have been proposed to explain the O(2) insensitivity, including lack of a hydrogen bond donor and negative electrostatic fields to selectively destabilize bound O(2), distal steric hindrance of all bound ligands to the heme iron, and restriction of in-plane movements of the iron atom. RECENT ADVANCES Crystallographic structures of the gas sensors, Thermoanaerobacter tengcongensis heme-nitric oxide/oxygen-binding domain (Tt H-NOX(1)) or Nostoc puntiforme (Ns) H-NOX, and measurements of O(2) binding to site-specific mutants of Tt H-NOX and the truncated β subunit of sGC suggest the need for a H-bonding donor to facilitate O(2) binding. CRITICAL ISSUES However, the O(2) insensitivity of full length sGC with a site-specific replacement of isoleucine by a tyrosine on residue 145 and the very slow autooxidation of Ns H-NOX and cytochrome c' suggest that more complex mechanisms have evolved to exclude O(2) but retain high affinity NO binding. A combined graphical analysis of ligand binding data for libraries of heme sensors, globins, and model heme shows that the NO sensors dramatically inhibit the formation of six-coordinated NO, CO, and O(2) complexes by direct distal steric hindrance (cyt c'), proximal constraints of in-plane iron movement (sGC), or combinations of both following a sliding scale rule. High affinity NO binding in H-NOX proteins is achieved by multiple NO binding steps that produce a high affinity five-coordinate NO complex, a mechanism that also prevents NO dioxygenation. FUTURE DIRECTIONS Knowledge advanced by further extensive test of this "sliding scale rule" hypothesis should be valuable in guiding novel designs for heme based sensors.
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Affiliation(s)
- Ah-Lim Tsai
- Division of Hematology, University of Texas Health Science Center at Houston, Houston, Texas 77225, USA.
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Caillet-Saguy C, Piccioli M, Turano P, Lukat-Rodgers G, Wolff N, Rodgers KR, Izadi-Pruneyre N, Delepierre M, Lecroisey A. Role of the iron axial ligands of heme carrier HasA in heme uptake and release. J Biol Chem 2012; 287:26932-43. [PMID: 22700962 DOI: 10.1074/jbc.m112.366385] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hemophore protein HasA from Serratia marcescens cycles between two states as follows: the heme-bound holoprotein, which functions as a carrier of the metal cofactor toward the membrane receptor HasR, and the heme-free apoprotein fishing for new porphyrin to be taken up after the heme has been delivered to HasR. Holo- and apo-forms differ for the conformation of the two loops L1 and L2, which provide the axial ligands of the iron through His(32) and Tyr(75), respectively. In the apo-form, loop L1 protrudes toward the solvent far away from loop L2; in the holoprotein, closing of the loops on the heme occurs upon establishment of the two axial coordination bonds. We have established that the two variants obtained via single point mutations of either axial ligand (namely H32A and Y75A) are both in the closed conformation. The presence of the heme and one out of two axial ligands is sufficient to establish a link between L1 and L2, thanks to the presence of coordinating solvent molecules. The latter are stabilized in the iron coordination environment by H-bond interactions with surrounding protein residues. The presence of such a water molecule in both variants is revealed here through a set of different spectroscopic techniques. Previous studies had shown that heme release and uptake processes occur via intermediate states characterized by a Tyr(75)-iron-bound form with open conformation of loop L1. Here, we demonstrate that these states do not naturally occur in the free protein but can only be driven by the interaction with the partner proteins.
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Affiliation(s)
- Célia Caillet-Saguy
- Unité de RMN des Biomolecules (CNRS URA 2185), Institut Pasteur, 28 Rue du Docteur Roux, 75015 Paris, France.
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Murphy EJ, Maréchal A, Segal AW, Rich PR. CO binding and ligand discrimination in human myeloperoxidase. Biochemistry 2010; 49:2150-8. [PMID: 20146436 DOI: 10.1021/bi9021507] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite the fact that ferrous myeloperoxidase (MPO) can bind both O(2) and NO, its ability to bind CO has been questioned. UV/visible spectroscopy was used to confirm that CO induces small spectral shifts in ferrous MPO, and Fourier transform infrared difference spectroscopy showed definitively that these arose from formation of a heme ferrous-CO compound. Recombination rates after CO photolysis were monitored at 618 and 645 nm as a function of CO concentration and pH. At pH 6.3, k(on) and k(off) were 0.14 mM(-1) x s(-1) and 0.23 s(-1), respectively, yielding an unusually high K(D) of 1.6 mM. This affinity of MPO for CO is 10 times weaker than its affinity for O(2). The observed rate constant for CO binding increased with increasing pH and was governed by a single protonatable group with a pK(a) of 7.8. Fourier transform infrared spectroscopy revealed two different conformations of bound CO with frequencies at 1927 and 1942 cm(-1). Their recombination rate constants were identical, indicative of two forms of bound CO that are in rapid thermal equilibrium rather than two distinct protein populations with different binding sites. The ratio of bound states was pH-dependent (pK(a) approximately 7.4) with the 1927 cm(-1) form favored at high pH. Structural factors that account for the ligand-binding properties of MPO are identified by comparisons with published data on a range of other ligand-binding heme proteins, and support is given to the recent suggestion that the proximal His336 in MPO is in a true imidazolate state.
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Affiliation(s)
- Emma J Murphy
- Centre for Molecular Medicine, Division of Medicine, University College London, 5 University Street, London WC1E 6JJ, UK
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Varhač R, Tomášková N, Fabián M, Sedlák E. Kinetics of cyanide binding as a probe of local stability/flexibility of cytochrome c. Biophys Chem 2009; 144:21-6. [DOI: 10.1016/j.bpc.2009.06.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2009] [Revised: 05/30/2009] [Accepted: 06/01/2009] [Indexed: 10/20/2022]
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Bidwai AK, Ok EY, Erman JE. pH dependence of cyanide binding to the ferric heme domain of the direct oxygen sensor from Escherichia coli and the effect of alkaline denaturation. Biochemistry 2008; 47:10458-70. [PMID: 18771281 DOI: 10.1021/bi800872d] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The spectrum of the ferric heme domain of the direct oxygen sensor protein from Escherichia coli ( EcDosH) has been measured between pH 3.0 and 12.6. EcDosH undergoes acid denaturation with an apparent p K a of 4.24 +/- 0.05 and a Hill coefficient of 3.1 +/- 0.6 and reversible alkaline denaturation with a p K a of 9.86 +/- 0.04 and a Hill coefficient of 1.1 +/- 0.1. Cyanide binding to EcDosH has been investigated between pH 4 and 11. The EcDosH-cyanide complex is most stable at pH 9 with a K D of 0.29 +/- 0.06 microM. The kinetics of cyanide binding are monophasic between pH 4 and 8. At pH >or=8.5, the reaction is biphasic with the fast phase dependent upon the cyanide concentration and the slow phase independent of cyanide. The slow phase is attributed to conversion of denatured EcDosH to the native state, with a pH-independent rate of 0.052 +/- 0.006 s (-1). The apparent association rate constant for cyanide binding to EcDosH increases from 3.6 +/- 0.1 M (-1) s (-1) at pH 4 to 520 +/- 20 M (-1) s (-1) at pH 11. The dissociation rate constant averages (8.6 +/- 1.3) x 10 (-5) s (-1) between pH 5 and 9, increasing to (1.4 +/- 0.1) x 10 (-3) s (-1) at pH 4 and (2.5 +/- 0.1) x 10 (-3) s (-1) at pH 12.2. The mechanism of cyanide binding is consistent with preferential binding of the cyanide anion to native EcDosH. The reactions of imidazole and H 2O 2 with ferric EcDosH were also investigated and show little reactivity.
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Affiliation(s)
- Anil K Bidwai
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, USA
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Varhač R, Antalík M. Correlation of acid-induced conformational transition of ferricytochrome c with cyanide binding kinetics. J Biol Inorg Chem 2008; 13:713-21. [DOI: 10.1007/s00775-008-0357-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 02/16/2008] [Indexed: 10/22/2022]
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Caillet-Saguy C, Turano P, Piccioli M, Lukat-Rodgers GS, Czjzek M, Guigliarelli B, Izadi-Pruneyre N, Rodgers KR, Delepierre M, Lecroisey A. Deciphering the Structural Role of Histidine 83 for Heme Binding in Hemophore HasA. J Biol Chem 2008; 283:5960-70. [DOI: 10.1074/jbc.m703795200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Weiss R, Gold A, Terner J. Cytochromes c‘: Biological Models for the S = 3/2,5/2 Spin-State Admixture? Chem Rev 2006; 106:2550-79. [PMID: 16771459 DOI: 10.1021/cr040416l] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Raymond Weiss
- Laboratoire de Chimie Supramoléculaires, Institut de Science et d'Ingénierie Supramoléculaires, Université Louis Pasteur de Strasbourg, 8 Allée Gaspard Monge, B.P.70028, F-67083 Strasbourg Cedex, France
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Shibata N, Iba S, Misaki S, Meyer TE, Bartsch RG, Cusanovich MA, Morimoto Y, Higuchi Y, Yasuoka N. Basis for monomer stabilization in Rhodopseudomonas palustris cytochrome c' derived from the crystal structure. J Mol Biol 1998; 284:751-60. [PMID: 9826513 DOI: 10.1006/jmbi.1998.2190] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The crystal structure of an unusual monomeric cytochrome c' from Rhodopseudomonas palustris (RPCP) has been determined at 2.3 A resolution. RPCP has the four-helix (helices A, B, C and D) bundle structure similar to dimeric cytochromes c'. However the amino acid composition of the surface of helices A and B in RPCP is remarkably different from that of the dimeric cytochromes c'. This surface forms the dimer interface in the latter proteins. RPCP has seven charged residues on this surface contrary to the dimeric cytochromes c', which have only two or three charged groups on the corresponding surface. Moreover, hydrophobic residues on this surface of RPCP are two to three times fewer than in dimeric cytochromes c'. As a result of the difference in amino acid composition, the A-B surface of RPCP is rather hydrophilic compared with dimeric cytochromes c'. We thus suggest that RPCP is monomeric in solution because of the hydrophilic nature of the A-B surface. The amino acid composition of the A-B surface is similar to that of Rhodobacter capsulatus cytochrome c' (RCCP), which is an equilibrium admixture of monomer and dimer. The charge distribution of the A-B surface in RCCP, however, is considerably different from that of RPCP. Due to the difference, RCCP can form dimers by both ionic and hydrophobic interactions. These dimers are quite different from those in proteins which form strong dimers such as in Chromatium vinosum, Rhodospirillum rubrum, Rhodospirillum molischianum and Alcaligenes. Cytochrome c' can be classified into two types. Type 1 cytochromes c' have hydrophobic A-B surfaces and they are globular. The A-B surface of type 2 cytochromes c' is hydrophilic and they take a monomeric or flattened dimeric form.
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Affiliation(s)
- N Shibata
- Faculty of Science, Himeji Institute of Technology, Hyogo, 678-1297, Japan
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Zahn JA, Arciero DM, Hooper AB, Dispirito AA. Cytochrome c' of Methylococcus capsulatus Bath. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 240:684-91. [PMID: 8856071 DOI: 10.1111/j.1432-1033.1996.0684h.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Cytochrome c' was isolated from the obligate methylotroph Methylococcus capsulatus Bath. The native and subunit molecular masses of the cytochrome were 34.9 kDa and 16.2 kDa, respectively, with an isoelectric pH of 7.0. The amino acid composition and N-terminal amino acid sequence were consistent with identification of the protein as a cytochrome c'. The electron paramagnetic resonance spectrum of the monoheme cytochrome indicated the presence of a high spin, S = 5/2, heme center that is diagnostic of cytochromes c'. The optical absorption spectra of ferric or ferrous cytochrome c' were also characteristic of cytochromes c'. The ferrocytochrome bound carbon monoxide and nitric oxide, but not isocyanide, cyanide, or azide. Changes in physical properties due to binding of CO or NO to some other c'-type cytochromes have been interpreted as an indication of dimer dissociation. In the case of cytochrome c' from M. capsulatus Bath, analytical ultracentrifugation of the ferricytochrome, the ferrocytochrome, and the ferrocytochrome-CO complex indicate that the changes induced by binding of CO are conformational and are not consistent with dimer dissociation. EPR spectra show that cytochrome c' was reduced in the presence of hydroxylamine only when in a complex with cytochrome P-460. The value of the midpoint potential, Em 7.0, was -250 mV for cytochrome c' from M. capsulatus Bath, which is well below the range of values reported for other cytochromes c'. The values of midpoint potentials for cytochrome P-460 (Em 7.0 = -300 mV to -380 mV) and cytochrome C555 (Em 7.0 = +175 mV to +195 mV) are less than and greater than, respectively, the value for cytochrome c' and suggest the possibility that the latter may function as an electron shuttle between cytochrome P-460 and cytochrome C555.
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Affiliation(s)
- J A Zahn
- Department of Microbiology, Immunology, and Preventive Medicine, Iowa State University, Iowa 50011-3211, USA
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Tahirov TH, Misaki S, Meyer TE, Cusanovich MA, Higuchi Y, Yasuoka N. Concerted movement of side chains in the haem vicinity observed on ligand binding in cytochrome c' from rhodobacter capsulatus. NATURE STRUCTURAL BIOLOGY 1996; 3:459-64. [PMID: 8612077 DOI: 10.1038/nsb0596-459] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have determined the structure of n-butylisocyanide-bound Rhodobacter capsulatus cytochrome c'. This is the first example of a ligand-bound structure of a class IIa cytochrome c. Compared with the structure of native cytochrome c', there are significant conformational changes of amino acid residues in the haem vicinity, accompanied by a rearrangement of the hydrogen bonding pattern. The results suggest that rearrangements resulting from ligand binding could drive dimer dissociation in some species and also that the haem propionate may participate in proton transfer.
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Affiliation(s)
- T H Tahirov
- Department of Life Science, Faculty of Science, Himeji Institute of Technology, Hyogo, Japan
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Abstract
The cytochromes c' bind CO, alkylisocyanides and CN- with rate and equilibrium constants which are 10(2)- to 10(6)-fold smaller than other high-spin hemoproteins. The decreased affinity for exogenous ligands is largely associated with steric interactions at the heme coordination site. While CO and alkylisocyanides bind noncooperatively to the dimeric Rhodospirillum molischianum cytochrome c', CO, alkylisocyanides and CN- appear to bind cooperatively to the dimeric Chromatium vinosum cytochrome c' due to a ligand-linked dimer-monomer dissociation equilibrium. The differences between the cytochromes c' are thought to be due to differences in amino acid residues near the heme coordination site and subunit interface.
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Affiliation(s)
- R J Kassner
- Department of Chemistry, University of Illinois, Chicago 60680
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Motie M, Kassner RJ, Meyer TE, Cusanovich MA. Cyanide-linked dimer-monomer equilibrium of Chromatium vinosum ferric cytochrome c'. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1076:97-102. [PMID: 1846081 DOI: 10.1016/0167-4838(91)90225-o] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cyanide binding to Chromatium vinosum ferricytochrome c' has been studied to further investigate possible allosteric interactions between the subunits of this dimeric protein. Cyanide binding to C. vinosum cytochrome c' appears to be cooperative. However, the cyanide binding reaction is unusual in that the overall affinity of cyanide increases as the concentration of cytochrome c' decreases and that cyanide binding causes the ligated dimer to dissociate to monomers as shown by gel-filtration chromatography. Therefore, the cyanide binding properties of C. vinosum ferricytochrome c' are complicated by a cyanide-linked dimer to monomer dissociation equilibrium of the complexed protein. The dimer to monomer dissociation constant is 20-fold smaller than that for CO linked dissociation constant of ferrocytochrome c'. Furthermore, the pH dependence of both the intrinsic equilibrium binding constant and the dimer to monomer equilibrium dissociation constant was investigated over the pH range of 7.0 to 9.2 to examine the effect of any ionizable groups. The equilibrium constants did not exhibit a significant pH dependence over this pH range.
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Affiliation(s)
- M Motie
- Department of Chemistry, University of Illinois, Chicago 60680
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