Skip to main content
SpringerLink
Log in

Conversion of a heme-based oxygen sensor to a heme oxygenase by hydrogen sulfide: effects of mutations in the heme distal side of a heme-based oxygen sensor phosphodiesterase (Ec DOS)

  • Published:
BioMetals Aims and scope Submit manuscript

An Erratum to this article was published on 31 July 2013

Abstract

The heme-based oxygen-sensor phosphodiesterase from Escherichia coli (Ec DOS), is composed of an N-terminal heme-bound oxygen sensing domain and a C-terminal catalytic domain. Oxygen (O2) binding to the heme Fe(II) complex in Ec DOS substantially enhances catalysis. Addition of hydrogen sulfide (H2S) to the heme Fe(III) complex in Ec DOS also remarkably stimulates catalysis in part due to the heme Fe(III)–SH and heme Fe(II)–O2 complexes formed by H2S. In this study, we examined the roles of the heme distal amino acids, M95 (the axial ligand of the heme Fe(II) complex) and R97 (the O2 binding site in the heme Fe(II)–O2 complex) of the isolated heme-binding domain of Ec DOS (Ec DOS-PAS) in the binding of H2S under aerobic conditions. Interestingly, R97A and R97I mutant proteins formed an oxygen-incorporated modified heme, verdoheme, following addition of H2S combined with H2O2 generated by the reactions. Time-dependent mass spectroscopic data corroborated the findings. In contrast, H2S did not interact with the heme Fe(III) complex of M95H and R97E mutants. Thus, M95 and/or R97 on the heme distal side in Ec DOS-PAS significantly contribute to the interaction of H2S with the Fe(III) heme complex and also to the modification of the heme Fe(III) complex with reactive oxygen species. Importantly, mutations of the O2 binding site of the heme protein converted its function from oxygen sensor to that of a heme oxygenase. This study establishes the novel role of H2S in modifying the heme iron complex to form verdoheme with the aid of reactive oxygen species.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Abbreviations

Ec DOS:

A heme-based oxygen-sensor phosphodiesterase from Escherichia coli

Ec DOS-PAS:

Isolated heme-bound PAS domain of Ec DOS

H2S:

Hydrogen sulfide

Heme Fe(II) complex:

Protoporphyrin IX ferrous complex

Heme Fe(III) complex:

Protoporphyrin IX ferric complex

MALDI TOF MS:

Matrix-assisted laser desorption/ionization

MS:

Mass spectrometry

PAS:

An acronym formed from Per (Drosophila period clock protein)-Arnt (vertebrate aryl hydrocarbon receptor nuclear translocator)-Sim (Drosophila single-minded protein)

SOD:

Superoxide dismutase

References

  • Andersson LA, Loehr TM, Lim AR, Mauk AG (1984) Sulfmyoglobin. Resonance Raman spectroscopic evidence for an iron-chlorin prosthetic group. J Biol Chem 259:15340–15349

    PubMed  CAS  Google Scholar 

  • Bailly X, Vinogradov S (2005) The sulfide binding function of annelid hemoglobins: relic of an old biosystem? J Inorg Biochem 99:142–150

    Article  PubMed  CAS  Google Scholar 

  • Banerjee R (2012) Hydrogen sulfide: redox metabolism and signaling. Antioxid Redox Signal 17:45–57

    Article  Google Scholar 

  • Berzofsky JA, Peisach J, Blumber WE (1971a) Sulfheme proteins. I. Optical and magnetic properties of sulfmyoglobin and its derivatives. J Biol Chem 246:3367–3377

    PubMed  CAS  Google Scholar 

  • Berzofsky JA, Peisach J, Blumberg WE (1971b) Sulfheme proteins. II. The reversible oxygenation of ferrous sulfmyoglobin. J Biol Chem 246:7366–7372

    PubMed  CAS  Google Scholar 

  • Evans SV, Sishta BP, Mauk AG, Brayer GD (1994) Three-dimensional structure of cyanomet-sulfmyoglobin C. Proc Nat Acad Sci USA 91:4723–4726

    Article  PubMed  CAS  Google Scholar 

  • Hewson WD, Hager LP (1979) Oxidation of horseradish peroxidase compound II to compound I. J Biol Chem 254:3182–3186

    PubMed  CAS  Google Scholar 

  • Hirata S, Matsui T, Sasakura Y, Sugiyama S, Yoshimura T, Sagami I, Shimizu T (2003) Characterization of Met95 mutants of a heme-regulated phosphodiesterase from Escherichia coli: optical absorption, magnetic circular dichroism, circular dichroism, and redox potentials. Eur J Biochem 270:4771–4779

    Article  PubMed  CAS  Google Scholar 

  • Igarashi J, Kitanishi K, Shimizu T (2011) Emerging role of heme as a signal and the gas-sensing site: heme-sensing and gas-sensing proteins. In: Kadish KM, Smith KM, Guilard R (eds) Handbook of porphyrin science, vol 15. World Scientific Hackensack, USA, pp 399–460

    Google Scholar 

  • Ishitsuka Y, Araki Y, Tanaka A, Igarashi J, Ito O, Shimizu T (2008) Arg97 at the heme-distal side of the isolated heme-bound PAS domain of a heme-based oxygen sensor from Escherichia coli (Ec DOS) plays critical roles in autooxidation and binding of gases, particularly O2. Biochemistry 47:8874–8884

    Article  PubMed  CAS  Google Scholar 

  • Kabil O, Banerjee R (2010) Redox biochemistry of hydrogen sulfide. J Biol Chem 285:21903–21907

    Article  PubMed  CAS  Google Scholar 

  • Kimura H, Shibuya N, Kimura Y (2012) Hydrogen sulfide is a signaling molecule and a cytoprotectant. Antioxid Redox Signal 17:45–57

    Article  PubMed  CAS  Google Scholar 

  • Kitanishi K, Kobayashi K, Kawamura Y, Ishigami I, Ogura T, Nakajima K, Igarashi J, Tanaka A, Shimizu T (2010) Important roles of Tyr43 at the putative heme distal side in the oxygen recognition and stability of the Fe(II)-O2 complex of YddV, a globin-coupled heme-based oxygen sensor diguanylate cyclase. Biochemistry 49:10381–10393

    Article  PubMed  CAS  Google Scholar 

  • Kitanishi K, Kobayashi K, Uchida T, Ishimori K, Igarashi J, Shimizu T (2011) Identification and functional and spectral characterization of a globin-coupled histidine kinase from Anaeromyxobacter sp. Fw109-5. J Biol Chem 286:35522–35534

    Article  PubMed  CAS  Google Scholar 

  • Kraus DW, Wittenberg JB (1990) Hemoglobins of the Lucina pectinata/bacteria symbiosis. I. Molecular properties, kinetics and equilibria of reactions with ligands. J Biol Chem 265:16043–16053

    PubMed  CAS  Google Scholar 

  • Kraus DW, Wittenberg JB, Jin-Fen L, Peisach J (1990) Hemoglobins of the Lucina pectinata/bateria symbiosis. II. An electron paramagnetic resonance and optical spectral study of the ferric proteins. J Biol Chem 265:16054–16059

    PubMed  CAS  Google Scholar 

  • Kurokawa H, Lee DS, Watanabe M, Sagami I, Mikami B, Raman CS, Shimizu T (2004) A redox-controlled molecular switch revealed by the crystal structure of a bacterial heme PAS sensor. J Biol Chem 279:20186–20193

    Article  PubMed  CAS  Google Scholar 

  • Lloyd E, Mauk AG (1994) Formation of sulphmyoglobin during expression of horse heart myoglobin in Escherichia coli. FEBS Lett 340:281–286

    Article  PubMed  CAS  Google Scholar 

  • Matsui T, Ozaki S, Watanabe Y (1997) On the formation and reactivity of compound I of the His-64 myoglobin mutants. J Biol Chem 272:32735–32738

    Article  PubMed  CAS  Google Scholar 

  • Matsui T, Iwasaki M, Sugiyama R, Unno M, Ikeda-Saito M (2010) Dioxygen activation for the self-degradation of heme: reaction mechanism and regulation of heme oxygenase. Inorg Chem 49:3602–3609

    Article  PubMed  CAS  Google Scholar 

  • Nicoletti FP, Comandini A, Bonamore A, Boechi L, Boubeta FM, Feis A, Smulvich G, Boffi A (2010) Sulfide binding properties of truncated hemoglobin. Biochemistry 49:2269–2278

    Article  PubMed  CAS  Google Scholar 

  • Ortiz de Montellano PR (1998) Heme oxygenase mechanistic evidence for an electrophilic ferric peroxide species. Acc Chem Res 31:543–549

    Article  CAS  Google Scholar 

  • Park H, Suquet C, Satterlee JD, Kang C (2004) Insights into signal transduction involving PAS domain oxygen-sensing heme proteins from the X-ray crystal structure of Escherichia coli DOS heme domain (Ec DOSH). Biochemistry 43:2738–2746

    Article  PubMed  CAS  Google Scholar 

  • Paul BD, Snyder SH (2012) H2S signalling through protein sulfhydration and beyond. Nat Rev Mol Cell Biol 13:499–507

    Article  PubMed  CAS  Google Scholar 

  • Pietri R, Lewis A, León RG, Casanoba G, Kiger L, Yeh SR, Ferdandez-Alberti S, Marden MC, Cadilla CL, López-Garriga J (2009) Factors controlling the reactivity of hydrogen sulfide with hemeproteins. Biochemistry 48:4881–4891

    Article  PubMed  CAS  Google Scholar 

  • Pietri R, Román-Morales E, López-Garriga J (2011) Hydrogen sulfide and hemeproteins: knowledge and mysteries. Antioxid Redox Signal 15:393–404

    Article  PubMed  CAS  Google Scholar 

  • Ragsdale SW, Yi L (2011) Thiol/disulfide redox switches in the regulation of heme binding to proteins. Antioxid Redox Signal 14:1039–1047

    Article  PubMed  CAS  Google Scholar 

  • Román-Morales E, Pietri R, Ramos-Santana B, Vinogradov SN, Lewis-Ballester A, López-Garriga J (2010) Structural determinants for the formation of sulfhemeprotein complexes. Biochem Biophys Res Commun 400:489–492

    Article  PubMed  Google Scholar 

  • Sakamoto H, Omata Y, Adachi Y, Palmer G, Noguchi M (2000) Separation and identification of regioisomers of verdoheme by reverse-phase ion-pair high-performance liquid chromatography, and characterization of their complexes with heme oxygenase. J Inorg Biochem 82:113–121

    Article  PubMed  CAS  Google Scholar 

  • Sasakura Y, Yoshimura-Suzuki T, Kurokawa H, Shimizu T (2006) Structure-function relationships of EcDOS, a heme-regulated phosphodiesterase from Escherichia coli. Acc Chem Res 39:37–43

    Article  PubMed  CAS  Google Scholar 

  • Shikama K (1998) The molecular mechanism of autooxidation for myoglobin and hemoglobin: a venerable puzzle. Chem Rev 98:1357–1374

    Article  PubMed  CAS  Google Scholar 

  • Shimizu T (2012) Binding of cysteine thiolate to the Fe(III) heme complex is critical for the function of heme sensor proteins. J Inorg Biochem 108:171–177

    Article  PubMed  CAS  Google Scholar 

  • Springer BA, Sligar SG, Olson JS, Phillips GN Jr (1994) Mechanisms of ligand recognition in myoglobin. Chem Rev 94:699–714

    Article  CAS  Google Scholar 

  • Sugishima M, Moffat K, Noguchi M (2012) Discrimination between CO and O2 in heme oxygenase: comparison of static structures and dynamic conformation changes following CO photolysis. Biochemistry 51:8554–8562

    Article  PubMed  CAS  Google Scholar 

  • Szabo C (2007) Hydrogen sulphide and its therapeutic potential. Nature Rev Drug Disco 6:917–935

    Article  CAS  Google Scholar 

  • Szabo C (2010) Gaseotransmitters: new frontiers for translational science. Sci Transl Med 2(59):ps54

    Article  Google Scholar 

  • Taguchi S, Matsui T, Igarashi J, Sasakura Y, Araki Y, Ito O, Sugiyama S, Sagami I, Shimizu T (2004) Binding of oxygen and carbon monoxide to a heme-regulated phosphodiesterase from Escherichia coli: kinetics and infrared spectra of the full-length wild-type enzyme, isolated PAS domain, and Met95 mutants. J Biol Chem 279:3340–3347

    Article  PubMed  CAS  Google Scholar 

  • Takahashi H, Sekimoto M, Tanaka M, Tanaka A, Igarashi J, Shimizu T (2012) Hydrogen sulfide stimulates the catalytic activity of a heme-regulated phosphodiesterase from Escherichia coli (Ec DOS). J Inorg Biochem 109:66–71

    Article  PubMed  CAS  Google Scholar 

  • Tanaka A, Shimizu T (2008) Ligand binding to the Fe(III)-protoporphyrin IX complex of phosphodiesterase from Escherichia coli (Ec DOS) markedly enhances catalysis of cyclic di-GMP: roles of Met95, Arg97, and Phe113 of the putative heme distal side in catalytic regulation and ligand binding. Biochemistry 47:13438–13446

    Article  PubMed  CAS  Google Scholar 

  • Tanaka A, Takahashi H, Shimizu T (2007) Critical role of the heme axial ligand, Met95, in locking catalysis of the phosphodiesterase from Escherichia coli (Ec DOS) toward cyclic diGMP. J Biol Chem 282:21301–21307

    Article  PubMed  CAS  Google Scholar 

  • Wang R (2010) Hydrogen sulfide: the third gaseotransmitter in biology and medicine. Antioxid Redox Signal 12:1061–1064

    Article  PubMed  CAS  Google Scholar 

  • Watanabe M, Matsui T, Sasakura Y, Sagami I, Shimizu T (2002) Unusual cyanide bindings to a heme-regulated phosphodiesterase from Escherichia coli: effect of Met95 mutations. Biochem Biophys Res Commun 299:169–172

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This work was in part supported by Grants-in-Aid from Shantou University Medical College and from the National Natural Science Foundation of China (NSFC) (No. 31170736) (to T. S.), and by Charles University in Prague (UNCE 204025/2012) (to M. M.).

Author information

Authors and Affiliations

  1. Department of Cell Biology, Shantou University Medical College, 22 Xinling Road, Shantou, 515041, Guangdong, China

    Yongming Du, Gefei Liu, Yinxia Yan, Dongyang Huang & Toru Shimizu

  2. Bioanalytical Laboratory, Shantou University Medical College, 22 Xinling Road, Shantou, 515041, Guangdong, China

    Wenhong Luo

  3. Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova (Albertov), 2030/8, Prague 2, Czech Republic

    Marketa Martinkova, Petr Man & Toru Shimizu

  4. Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Videnska 1083, Prague 4, Czech Republic

    Petr Man

Authors
  1. Yongming Du
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Gefei Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yinxia Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Dongyang Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Wenhong Luo
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Marketa Martinkova
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Petr Man
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Toru Shimizu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Toru Shimizu.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 57 kb)

Supplementary material 2 (PPT 2569 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Du, Y., Liu, G., Yan, Y. et al. Conversion of a heme-based oxygen sensor to a heme oxygenase by hydrogen sulfide: effects of mutations in the heme distal side of a heme-based oxygen sensor phosphodiesterase (Ec DOS). Biometals 26, 839–852 (2013). https://doi.org/10.1007/s10534-013-9640-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10534-013-9640-4

Keywords

Search

Navigation