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Influence of the heme distal pocket on nitrite binding orientation and reactivity in Sperm Whale myoglobin. Biochem J 2021; 478:927-942. [PMID: 33543749 PMCID: PMC7925009 DOI: 10.1042/bcj20200596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/30/2021] [Accepted: 02/05/2021] [Indexed: 12/05/2022]
Abstract
Nitrite binding to recombinant wild-type Sperm Whale myoglobin (SWMb) was studied using a combination of spectroscopic methods including room-temperature magnetic circular dichroism. These revealed that the reactive species is free nitrous acid and the product of the reaction contains a nitrite ion bound to the ferric heme iron in the nitrito- (O-bound) orientation. This exists in a thermal equilibrium with a low-spin ground state and a high-spin excited state and is spectroscopically distinct from the purely low-spin nitro- (N-bound) species observed in the H64V SWMb variant. Substitution of the proximal heme ligand, histidine-93, with lysine yields a novel form of myoglobin (H93K) with enhanced reactivity towards nitrite. The nitrito-mode of binding to the ferric heme iron is retained in the H93K variant again as a thermal equilibrium of spin-states. This proximal substitution influences the heme distal pocket causing the pKa of the alkaline transition to be lowered relative to wild-type SWMb. This change in the environment of the distal pocket coupled with nitrito-binding is the most likely explanation for the 8-fold increase in the rate of nitrite reduction by H93K relative to WT SWMb.
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2
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Tilleman L, Germani F, De Henau S, Helbo S, Desmet F, Berghmans H, Van Doorslaer S, Hoogewijs D, Schoofs L, Braeckman BP, Moens L, Fago A, Dewilde S. A globin domain in a neuronal transmembrane receptor of Caenorhabditis elegans and Ascaris suum: molecular modeling and functional properties. J Biol Chem 2015; 290:10336-52. [PMID: 25666609 DOI: 10.1074/jbc.m114.576520] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Indexed: 01/12/2023] Open
Abstract
We report the structural and biochemical characterization of GLB-33, a putative neuropeptide receptor that is exclusively expressed in the nervous system of the nematode Caenorhabditis elegans. This unique chimeric protein is composed of a 7-transmembrane domain (7TM), GLB-33 7TM, typical of a G-protein-coupled receptor, and of a globin domain (GD), GLB-33 GD. Comprehensive sequence similarity searches in the genome of the parasitic nematode, Ascaris suum, revealed a chimeric protein that is similar to a Phe-Met-Arg-Phe-amide neuropeptide receptor. The three-dimensional structures of the separate domains of both species and of the full-length proteins were modeled. The 7TM domains of both proteins appeared very similar, but the globin domain of the A. suum receptor surprisingly seemed to lack several helices, suggesting a novel truncated globin fold. The globin domain of C. elegans GLB-33, however, was very similar to a genuine myoglobin-type molecule. Spectroscopic analysis of the recombinant GLB-33 GD showed that the heme is pentacoordinate when ferrous and in the hydroxide-ligated form when ferric, even at neutral pH. Flash-photolysis experiments showed overall fast biphasic CO rebinding kinetics. In its ferrous deoxy form, GLB-33 GD is capable of reversibly binding O2 with a very high affinity and of reducing nitrite to nitric oxide faster than other globins. Collectively, these properties suggest that the globin domain of GLB-33 may serve as a highly sensitive oxygen sensor and/or as a nitrite reductase. Both properties are potentially able to modulate the neuropeptide sensitivity of the neuronal transmembrane receptor.
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Affiliation(s)
| | | | - Sasha De Henau
- the Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Signe Helbo
- the Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark
| | - Filip Desmet
- Physics, University of Antwerp, 2610 Antwerp, Belgium
| | | | | | - David Hoogewijs
- the Institute of Physiology and Zürich Center for Integrative Human Physiology, University of Zürich, 8006 Zürich, Switzerland, Institute of Physiology, University of Duisburg-Essen, D-45147 Essen, Germany, and
| | - Liliane Schoofs
- the Functional Genomics and Proteomics Group, KU Leuven, 3000 Leuven, Belgium
| | - Bart P Braeckman
- the Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Luc Moens
- From the Departments of Biomedical Sciences and
| | - Angela Fago
- the Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark
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3
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Bradley JM, Silkstone G, Wilson MT, Cheesman MR, Butt JN. Probing a Complex of Cytochrome c and Cardiolipin by Magnetic Circular Dichroism Spectroscopy: Implications for the Initial Events in Apoptosis. J Am Chem Soc 2011; 133:19676-9. [DOI: 10.1021/ja209144h] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Justin M. Bradley
- Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, U.K
| | - Gary Silkstone
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, U.K
| | - Michael T. Wilson
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, U.K
| | - Myles R. Cheesman
- Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, U.K
| | - Julea N. Butt
- Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, U.K
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Terner J, Palaniappan V, Gold A, Weiss R, Fitzgerald MM, Sullivan AM, Hosten CM. Resonance Raman spectroscopy of oxoiron(IV) porphyrin π-cation radical and oxoiron(IV) hemes in peroxidase intermediates. J Inorg Biochem 2006; 100:480-501. [PMID: 16513173 DOI: 10.1016/j.jinorgbio.2006.01.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Accepted: 01/04/2006] [Indexed: 11/15/2022]
Abstract
The catalytic cycle intermediates of heme peroxidases, known as compounds I and II, have been of long standing interest as models for intermediates of heme proteins, such as the terminal oxidases and cytochrome P450 enzymes, and for non-heme iron enzymes as well. Reports of resonance Raman signals for compound I intermediates of the oxo-iron(IV) porphyrin pi-cation radical type have been sometimes contradictory due to complications arising from photolability, causing compound I signals to appear similar to those of compound II or other forms. However, studies of synthetic systems indicated that protein based compound I intermediates of the oxoiron(IV) porphyrin pi-cation radical type should exhibit vibrational signatures that are different from the non-radical forms. The compound I intermediates of horseradish peroxidase (HRP), and chloroperoxidase (CPO) from Caldariomyces fumago do in fact exhibit unique and characteristic vibrational spectra. The nature of the putative oxoiron(IV) bond in peroxidase intermediates has been under discussion in the recent literature, with suggestions that the Fe(IV)O unit might be better described as Fe(IV)-OH. The generally low Fe(IV)O stretching frequencies observed for proteins have been difficult to mimic in synthetic ferryl porphyrins via electron donation from trans axial ligands alone. Resonance Raman studies of iron-oxygen vibrations within protein species that are sensitive to pH, deuteration, and solvent oxygen exchange, indicate that hydrogen bonding to the oxoiron(IV) group within the protein environment contributes to substantial lowering of Fe(IV)O frequencies relative to those of synthetic model compounds.
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Affiliation(s)
- James Terner
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA.
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Papadopoulou ND, Mewies M, McLean KJ, Seward HE, Svistunenko DA, Munro AW, Raven EL. Redox and spectroscopic properties of human indoleamine 2,3-dioxygenase and a His303Ala variant: implications for catalysis. Biochemistry 2005; 44:14318-28. [PMID: 16245948 DOI: 10.1021/bi0513958] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Indoleamine 2,3-dioxygenase is an important mammalian target that catalyses the oxidative cleavage of l-tryptophan to N-formylkynurenine. In this work, the redox properties of recombinant human indoleamine 2,3-dioxygenase (rhIDO) and its H303A variant have been examined for the first time and the spectroscopic and substrate-binding properties of rhIDO and H303A in the presence and absence of substrate are reported. The Fe(3+)/Fe(2+) reduction potential of H303A was found to be -30 +/- 4 mV; in the presence of l-Trp, this value increases to +16 +/- 3 mV. A variety of spectroscopies indicate that ferric rhIDO at pH 6.6 exists as a mixture of six-coordinate, high-spin, water-bound heme and a low-spin species that contains a second nitrogenous ligand; parallel experiments on H303A are consistent either with His303 as the sixth ligand or with His303 linked to a conformational change that affects this transition. There is an increase in the low-spin component at alkaline pH for rhIDO, but this is not due to hydroxide-bound heme. Substrate binding induces a conformational rearrangement and formation of low-spin, hydroxide-bound heme; analysis of the H303A variant indicates that His303 is not required for this conversion and is not essential for substrate binding. The Fe(3+)/Fe(2+) reduction potential of H303A variant is approximately 70 mV lower than that of rhIDO, leading to a destabilization of the ferrous-oxy complex, which is an obligate intermediate in the catalytic process. In comparison with the properties of other heme enzymes, the data can be used to build a more detailed picture of substrate binding and catalysis in indoleamine 2,3-dioxygenase. The wider implications of these results are discussed in the context of our current understanding of the catalytic mechanism of the enzyme.
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Affiliation(s)
- Nektaria D Papadopoulou
- Department of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH, United Kingdom
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Jones DK, Patel N, Cheesman MR, Thomson AJ, Raven EL. Leghaemoglobin: a model for the investigation of haem protein axial ligation. Inorganica Chim Acta 2002. [DOI: 10.1016/s0020-1693(02)00689-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sanders SA, Bray RC, Smith AT. pH-dependent properties of a mutant horseradish peroxidase isoenzyme C in which Arg38 has been replaced with lysine. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 224:1029-37. [PMID: 7925400 DOI: 10.1111/j.1432-1033.1994.01029.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Arg38 in the active site of horseradish peroxidase isoenzyme C (HRP-C) has been replaced with lysine by site-directed mutagenesis. As a preclude to a detailed kinetic analysis of this variant, the present study characterizes a pH-dependent cycle of reactions for recombinant horseradish peroxidase isoenzyme C with Arg38 replaced by lysine ([R38K]HRP-C*), which involves time-dependent changes in both specific activity and the electronic absorption spectrum of the enzyme. This pH-dependent cycle resembles that previously suggested for a cytochrome-c peroxidase variant in which Asp235 was replaced with asparagine. When the pH of a solution of resting [R38K]HRP-C* at pH 6.6 (form AH) is raised to pH 8.6, a rapid alkaline transition occurs. This results in spectral changes characteristic of a shift from a predominantly pentacoordinate to a completely hexacoordinate high-spin haem iron (form A-) with a pKa of 7.5. When the pH of a solution of form A- is raised from 8.7 to 12.0, no further spectral changes are observed. The reaction is reversible, but when the high-pH form of the enzyme (A-) is allowed to stand at pH 8.6, it slowly becomes converted into a third enzyme form (form I-) at a rate which is independent of pH (k = 0.56 h-1). When the pH of a sample of form I- is lowered from 8.6 to 6.6, the original low-pH form (AH) of the enzyme is recovered. Recovery of form AH from form I- does not occur via form A-, but via at least one further intermediate, form X. Following a downward pH jump, the rate constant for the formation of form X from form I- shows a small dependence on pH, changing from 48 s-1 at pH 6.8 to 39 s-1 at pH 7.4. The rate of formation of form AH from form X is also pH dependent and biphasic in nature, with measured rate constants ranging from 11.9-2.1 h-1. The possible structures of the different forms of [R38K]HRP-C* are discussed in the light of similar data in the literature for variants of cytochrome-c peroxidase. The properties may be indicative of a greater degree of conformational flexibility within the active site of this mutant caused by the smaller bulk of the lysine side-chain and the probable disruption of a part of the haem-linked hydrogen-bonding network in the distal haem pocket. The wild-type enzyme undergoes no such pH induced changes.
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Affiliation(s)
- S A Sanders
- Biochemistry Laboratory, School of Biological Sciences, University of Sussex, Brighton, England
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Feis A, Marzocchi MP, Paoli M, Smulevich G. Spin state and axial ligand bonding in the hydroxide complexes of metmyoglobin, methemoglobin, and horseradish peroxidase at room and low temperatures. Biochemistry 1994; 33:4577-83. [PMID: 8161513 DOI: 10.1021/bi00181a019] [Citation(s) in RCA: 106] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Absorption and resonance Raman spectra using Soret excitation of alkaline metmyoglobin (metMb), methemoglobin (metHb), and horseradish peroxidase (HRP) were obtained at room and low temperature. At 298 K both metMb and metHb exhibit two isotope-sensitive bands assigned to high- and low-spin nu(Fe-OH) stretching modes, respectively, which are correlated with the spin-state population. The low-spin stretch occurs 60 cm-1 to higher energy than the corresponding high-spin vibration. When the temperature is lowered, only the low-spin species is observed. HRP exhibits at both 298 and 20 K only the low-spin nu(Fe-OH) stretching mode, which occurs 50 cm-1 to lower energy than the corresponding modes observed in the globins. This is explained in the context of a strong hydrogen bond between the hydroxyl ligand and the distal His42 and/or Arg38. Lowering temperature causes in all of the examined proteins a strengthening of the Fe-OH bond and a contraction of the core of about 0.01 A, as determined by the upshifting of the low-spin nu(Fe-OH) stretching mode and the core size marker bands. Both effects are ascribed to an increase of the packing forces.
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Affiliation(s)
- A Feis
- Università di Firenze, Dipartimento di Chimica, Italy
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10
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Chuang W, Van Wart H. Resonance Raman spectra of horseradish peroxidase and bovine liver catalase compound I species. Evidence for predominant 2A2u pi-cation radical ground state configurations. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)42209-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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11
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Simulations of the g-strain broadening of low-spin hemoprotein EPR spectra based on the t2g hole model. ACTA ACUST UNITED AC 1990. [DOI: 10.1016/0022-2364(90)90053-c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Foote N, Gadsby PM, Greenwood C, Thomson AJ. pH-dependent forms of the ferryl haem in myoglobin peroxide analysed by variable-temperature magnetic circular dichroism. Biochem J 1989; 261:515-22. [PMID: 2775230 PMCID: PMC1138856 DOI: 10.1042/bj2610515] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The reaction product of myoglobin and H2O2 exists in two different forms according to the external pH. Varied-temperature magnetic-circular dichroism (m.c.d.) spectroscopy demonstrates that both contain the oxyferryl ion Fe(IV) = O. Alkaline myoglobin peroxide has often been used as a model for oxidized intermediates in the catalytic cycles of haem-containing peroxidases, but absorption and m.c.d. spectra show that the acid form is much more closely related to species such as horeradish peroxidase Compound II. The differences are tentatively ascribed to ionization of the proximal histidine ligand in alkaline myoglobin peroxide. It is also shown that the m.c.d. method allows an estimate of the zero-field splitting parameter of both forms, values of D = 28.0 +/- 3 cm-1 and 35.0 +/- 5 cm-1 being obtained for the alkaline and acid forms respectively.
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Affiliation(s)
- N Foote
- School of Biological Sciences, University of East Anglia, Norwich, U.K
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