Skip to content
Licensed Unlicensed Requires Authentication Published by De Gruyter January 8, 2014

The redox properties of the unique heme in cystathionine β-synthase

  • Ernesto Cuevasanta , Sebastián Carballal , Martín Graña EMAIL logo and Beatriz Alvarez EMAIL logo

Abstract

Cystathionine β-synthase (CBS) catalyzes the condensation of homocysteine with serine or cysteine to form cystathionine and H2O or H2S. Human CBS has a non-catalytic heme bound to cysteine and histidine. The heme environment is conserved among several eukaryotic species but does not resemble any other protein. Fe(III)-CBS is relatively unreactive; however, reduction to Fe(II)-CBS can be achieved by strong chemical and biochemical reductants. Once reduced, Fe(II)-CBS can react with CO, which leads to a carbonylated and inactive species. Fe(II)-CBS can also be reoxidized by oxygen back to Fe(III)-CBS, thus forming superoxide radical. Kinetic considerations favor reoxidation unless this occurs under very low oxygen concentrations.


Corresponding authors: Beatriz Alvarez, Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay, e-mail: ; and Martín Graña, Unidad de Bioinformática, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay, e-mail:

  1. 1

    The NR and RefSeq databases from NCBI as well as the complete and curated eukaryotic proteomes stored at UniProt were first surveyed with BLAST (Altschul et al., 1990). More distant homologs were searched by way of iterative methods, namely, CS-BLAST (Biegert and Soding, 2009), HHSenser (Soding et al., 2006), and HHBlits (Remmert et al., 2011). Multiple sequence alignments were computed with MAFFT (Katoh and Toh, 2008), T-COFFEE (Notredame et al., 2000), and Prank (Loytynoja and Goldman, 2005).

  2. 2

    Structural similarity searches were carried out with DALI (Holm and Sander, 1995), SSM (Krissinel and Henrick, 2004), and VAST (Gibrat et al., 1996).

This work was supported by grants from CSIC, Universidad de la República, Uruguay (to B. A.), a fellowship from ANII (Agencia Nacional de Investigación e Innovación, Uruguay) (to E. C. and S. C.) and grant FCE_2009_377, also from ANII (to M. G.).

References

Abe K.; Kimura H. The possible role of hydrogen sulfide as an endogenous neuromodulator. J. Neurosci. 1996, 16, 1066–1071.Search in Google Scholar

Altschul S. F.; Gish W.; Miller W.; Myers E. W.; Lipman D. J. Basic local alignment search tool. J. Mol. Biol. 1990, 215, 403–410.Search in Google Scholar

Biegert A.; Soding J. Sequence context-specific profiles for homology searching. Proc. Natl. Acad. Sci. USA 2009, 106, 3770–3775.10.1073/pnas.0810767106Search in Google Scholar PubMed PubMed Central

Carballal S.; Madzelan P.; Zinola C. F.; Graña M.; Radi R.; Banerjee R.; Alvarez B. Dioxygen reactivity and heme redox potential of truncated human cystathionine beta-synthase. Biochemistry 2008, 47, 3194–3201.Search in Google Scholar

Carballal S.; Cuevasanta E.; Marmisolle I.; Kabil O.; Gherasim C.; Ballou D. P.; Banerjee R.; Alvarez B. Kinetics of reversible reductive carbonylation of heme in human cystathionine β-synthase. Biochemistry 2013, 52, 4553–4562.Search in Google Scholar

Celano L.; Gil M.; Carballal S.; Duran R.; Denicola A.; Banerjee R.; Alvarez B. Inactivation of cystathionine beta-synthase with peroxynitrite. Arch. Biochem. Biophys. 2009, 491, 96–105.Search in Google Scholar

Cherney M. M.; Pazicni S.; Frank N.; Marvin K. A.; Kraus J. P.; Burstyn J. N. Ferrous human cystathionine beta-synthase loses activity during enzyme assay due to a ligand switch process. Biochemistry 2007, 46, 13199–13210.Search in Google Scholar

Clarke R.; Smith A. D.; Jobst K. A.; Refsum H.; Sutton L.; Ueland P. M. Folate, vitamin B12, and serum total homocysteine levels in confirmed Alzheimer disease. Arch. Neurol. 1998, 55, 1449–1455.Search in Google Scholar

De Rosny E.; de Groot A.; Jullian-Binard C.; Gaillard J.; Borel F.; Pebay-Peyroula E.; Fontecilla-Camps J. C.; Jouve H. M. Drosophila nuclear receptor E75 is a thiolate hemoprotein. Biochemistry 2006, 45, 9727–9734.Search in Google Scholar

De Rosny E.; de Groot A.; Jullian-Binard C.; Borel F.; Suarez C.; Le Pape L.; Fontecilla-Camps J. C.; Jouve H. M. DHR51, the Drosophila melanogaster homologue of the human photoreceptor cell-specific nuclear receptor, is a thiolate heme-binding protein. Biochemistry 2008, 47, 13252–13260.Search in Google Scholar

Elrod J. W.; Calvert J. W.; Morrison J.; Doeller J. E.; Kraus D. W.; Tao L.; Jiao X.; Scalia R.; Kiss L.; Szabo C.; et al. Hydrogen sulfide attenuates myocardial ischemia-reperfusion injury by preservation of mitochondrial function. Proc. Natl. Acad. Sci. USA 2007, 104, 15560–15565.Search in Google Scholar

Evande R.; Ojha S.; Banerjee R. Visualization of PLP-bound intermediates in hemeless variants of human cystathionine beta-synthase: evidence that lysine 119 is a general base. Arch. Biochem. Biophys. 2004, 427, 188–196.Search in Google Scholar

Gibrat J. F.; Madej T.; Bryant S. H. Surprising similarities in structure comparison. Curr. Opin. Struct. Biol. 1996, 6, 377–385.Search in Google Scholar

Holm L.; Sander C. Dali: a network tool for protein structure comparison. Trends. Biochem. Sci. 1995, 20, 478–480.Search in Google Scholar

Igarashi J.; Murase M.; Iizuka A.; Pichierri F.; Martinkova M.; Shimizu T. Elucidation of the heme binding site of heme-regulated eukaryotic initiation factor 2alpha kinase and the role of the regulatory motif in heme sensing by spectroscopic and catalytic studies of mutant proteins. J. Biol. Chem. 2008, 283, 18782–18791.Search in Google Scholar

Ingi T.; Chiang G.; Ronnett G. V. The regulation of heme turnover and carbon monoxide biosynthesis in cultured primary rat olfactory receptor neurons. J. Neurosci. 1996, 16, 5621–5628.Search in Google Scholar

Kabil O.; Toaka S.; LoBrutto R.; Shoemaker R.; Banerjee R. Pyridoxal phosphate binding sites are similar in human heme-dependent and yeast heme-independent cystathionine beta-synthases. Evidence from 31P NMR and pulsed EPR spectroscopy that heme and PLP cofactors are not proximal in the human enzyme. J. Biol. Chem. 2001, 276, 19350–19355.Search in Google Scholar

Kabil O.; Vitvitsky V.; Xie P.; Banerjee R. The quantitative significance of the transsulfuration enzymes for H2S production in murine tissues. Antioxid. Redox Signal. 2011a, 15, 363–372.Search in Google Scholar

Kabil O.; Weeks C. L.; Carballal S.; Gherasim C.; Alvarez B.; Spiro T. G.; Banerjee R. Reversible heme-dependent regulation of human cystathionine beta-synthase by a flavoprotein oxidoreductase. Biochemistry. 2011b, 50, 8261–8263.Search in Google Scholar

Katoh K.; Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 2008, 9, 286–298.Search in Google Scholar

Kery V.; Bukovska G.; Kraus J. P. Transsulfuration depends on heme in addition to pyridoxal 5’-phosphate. Cystathionine beta-synthase is a heme protein. J. Biol. Chem. 1994, 269, 25283–25288.Search in Google Scholar

Kery V.; Poneleit L.; Kraus J. P. Trypsin cleavage of human cystathionine beta-synthase into an evolutionarily conserved active core: structural and functional consequences. Arch. Biochem. Biophys. 1998, 355, 222–232.Search in Google Scholar

Kilmartin J. R.; Maher M. J.; Krusong K.; Noble C. J.; Hanson G. R.; Bernhardt P. V.; Riley M. J.; Kappler U. Insights into structure and function of the active site of SoxAX cytochromes. J. Biol. Chem. 2011, 286, 24872–24881.Search in Google Scholar

Koutmos M.; Kabil O.; Smith J. L.; Banerjee R. Structural basis for substrate activation and regulation by cystathionine beta-synthase (CBS) domains in cystathionine {beta}-synthase. Proc. Natl. Acad. Sci. USA 2010, 107, 20958–20963.Search in Google Scholar

Kraus J. P.; Janosik M.; Kozich V.; Mandell R.; Shih V.; Sperandeo M. P.; Sebastio G.; de Franchis R.; Andria G.; Kluijtmans L. A.; et al. Cystathionine beta-synthase mutations in homocystinuria. Hum. Mutat. 1999, 13, 362–375.Search in Google Scholar

Krissinel E.; Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta. Crystallogr. Biol. Crystallogr. 2004, 60, 2256–2268.Search in Google Scholar

Loytynoja A.; Goldman N. An algorithm for progressive multiple alignment of sequences with insertions. Proc. Natl. Acad. Sci. USA 2005, 102, 10557–10562.10.1073/pnas.0409137102Search in Google Scholar PubMed PubMed Central

Marvin K. A.; Kerby R. L.; Youn H.; Roberts G. P.; Burstyn J. N. The transcription regulator RcoM-2 from Burkholderia xenovorans is a cysteine-ligated hemoprotein that undergoes a redox-mediated ligand switch. Biochemistry 2008, 47, 9016–9028.Search in Google Scholar

McCully K. S. Vascular pathology of homocysteinemia: implications for the pathogenesis of arteriosclerosis. Am. J. Pathol. 1969, 56, 111–128.Search in Google Scholar

Meier M.; Janosik M.; Kery V.; Kraus J. P.; Burkhard P. Structure of human cystathionine beta-synthase: a unique pyridoxal 5’-phosphate-dependent heme protein. EMBO J. 2001, 20, 3910–3916.Search in Google Scholar

Mills J. L.; McPartlin J. M.; Kirke P. N.; Lee Y. J.; Conley M. R.; Weir D. G.; Scott J. M. Homocysteine metabolism in pregnancies complicated by neural-tube defects. Lancet 1995, 345, 149–151.Search in Google Scholar

Morikawa T.; Kajimura M.; Nakamura T.; Hishiki T.; Nakanishi T.; Yukutake Y.; Nagahata Y.; Ishikawa M.; Hattori K.; Takenouchi T.; et al. Hypoxic regulation of the cerebral microcirculation is mediated by a carbon monoxide-sensitive hydrogen sulfide pathway. Proc. Natl. Acad. Sci. USA 2012, 109, 1293–1298.Search in Google Scholar

Notredame C.; Higgins D. G.; Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000, 302, 205–217.Search in Google Scholar

Ojha S.; Hwang J.; Kabil O.; Penner-Hahn J. E.; Banerjee R. Characterization of the heme in human cystathionine beta-synthase by X-ray absorption and electron paramagnetic resonance spectroscopies. Biochemistry 2000, 39, 10542–10547.Search in Google Scholar

Olteanu H.; Banerjee R. Human methionine synthase reductase, a soluble P-450 reductase-like dual flavoprotein, is sufficient for NADPH-dependent methionine synthase activation. J. Biol. Chem. 2001, 276, 35558–35563.Search in Google Scholar

Pardee K. I.; Xu X.; Reinking J.; Schuetz A.; Dong A.; Liu S.; Zhang R.; Tiefenbach J.; Lajoie G.; Plotnikov A. N.; et al. The structural basis of gas-responsive transcription by the human nuclear hormone receptor REV-ERBbeta. PLoS Biol. 2009, 7, e43.Search in Google Scholar

Pazicni S.; Cherney M. M.; Lukat-Rodgers G. S.; Oliveriusova J.; Rodgers K. R.; Kraus J. P.; Burstyn J. N. The heme of cystathionine beta-synthase likely undergoes a thermally induced redox-mediated ligand switch. Biochemistry 2005, 44, 16785–16795.Search in Google Scholar

Puranik M.; Weeks C. L.; Lahaye D.; Kabil O.; Taoka S.; Nielsen S. B.; Groves J. T.; Banerjee R.; Spiro T. G. Dynamics of carbon monoxide binding to cystathionine beta-synthase. J. Biol. Chem. 2006, 281, 13433–13438.Search in Google Scholar

Remmert M.; Biegert A.; Hauser A.; Soding J. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods 2011, 9, 173–175.Search in Google Scholar

Shintani T.; Iwabuchi T.; Soga T.; Kato Y.; Yamamoto T.; Takano N.; Hishiki T.; Ueno Y.; Ikeda S.; Sakuragawa T.; et al. Cystathionine beta-synthase as a carbon monoxide-sensitive regulator of bile excretion. Hepatology 2009, 49, 141–150.Search in Google Scholar

Singh S.; Madzelan P.; Banerjee R. Properties of an unusual heme cofactor in PLP-dependent cystathionine beta-synthase. Nat. Prod. Rep. 2007, 24, 631–639.Search in Google Scholar

Singh S.; Padovani D.; Leslie R. A.; Chiku T.; Banerjee R. Relative contributions of cystathionine beta-synthase and gamma-cystathionase to H2S biogenesis via alternative trans-sulfuration reactions. J. Biol. Chem. 2009a, 284, 22457–22466.Search in Google Scholar

Singh S.; Madzelan P.; Stasser J.; Weeks C. L.; Becker D.; Spiro T. G.; Penner-Hahn J.; Banerjee R. Modulation of the heme electronic structure and cystathionine beta-synthase activity by second coordination sphere ligands: The role of heme ligand switching in redox regulation. J. Inorg. Biochem. 2009b, 103, 689–697.Search in Google Scholar

Sitkovsky M.; Lukashev D. Regulation of immune cells by local-tissue oxygen tension: HIF1 alpha and adenosine receptors. Nat. Rev. Immunol. 2005, 5, 712–721.Search in Google Scholar

Smith A. T.; Su Y.; Stevens D. J.; Majtan T.; Kraus J. P.; Burstyn J. N. Effect of the Disease-Causing R266K Mutation on the Heme and PLP Environments of Human Cystathionine beta-Synthase. Biochemistry 2012a, 51, 6360–6370.10.1021/bi300421zSearch in Google Scholar PubMed PubMed Central

Smith A. T.; Marvin K. A.; Freeman K. M.; Kerby R. L.; Roberts G. P.; Burstyn J. N. Identification of Cys94 as the distal ligand to the Fe(III) heme in the transcriptional regulator RcoM-2 from Burkholderia xenovorans. J. Biol. Inorg. Chem. JBIC Publ. Soc. Biol. Inorg. Chem. 2012b, 17, 1071–1082.Search in Google Scholar

Soding J.; Remmert M.; Biegert A.; Lupas A. N. HHsenser: exhaustive transitive profile search using HMM-HMM comparison. Nucleic. Acids Res. 2006, 34, W374–W378.Search in Google Scholar

Taoka S.; Banerjee R. Characterization of NO binding to human cystathionine beta-synthase: possible implications of the effects of CO and NO binding to the human enzyme. J. Inorg. Biochem. 2001, 87, 245–251.Search in Google Scholar

Taoka S.; Ohja S.; Shan X.; Kruger W. D.; Banerjee R. Evidence for heme-mediated redox regulation of human cystathionine beta-synthase activity. J. Biol. Chem. 1998, 273, 25179–25184.Search in Google Scholar

Taoka S.; Widjaja L.; Banerjee R. Assignment of enzymatic functions to specific regions of the PLP-dependent heme protein cystathionine beta-synthase. Biochemistry 1999a, 38, 13155–13161.10.1021/bi990865tSearch in Google Scholar PubMed

Taoka S.; West M.; Banerjee R. Characterization of the heme and pyridoxal phosphate cofactors of human cystathionine beta-synthase reveals nonequivalent active sites. Biochemistry 1999b, 38, 2738.10.1021/bi9826052Search in Google Scholar PubMed

Taoka S.; Green E. L.; Loehr T. M.; Banerjee R. Mercuric chloride-induced spin or ligation state changes in ferric or ferrous human cystathionine beta-synthase inhibit enzyme activity. J. Inorg. Biochem. 2001, 87, 253–259.Search in Google Scholar

Taoka S.; Lepore B. W.; Kabil O.; Ojha S.; Ringe D.; Banerjee R. Human cystathionine beta-synthase is a heme sensor protein. Evidence that the redox sensor is heme and not the vicinal cysteines in the CXXC motif seen in the crystal structure of the truncated enzyme. Biochemistry 2002, 41, 10454–10461.Search in Google Scholar

Uchida T.; Sagami I.; Shimizu T.; Ishimori K.; Kitagawa T. Effects of the bHLH domain on axial coordination of heme in the PAS-A domain of neuronal PAS domain protein 2 (NPAS2): conversion from His119/Cys170 coordination to His119/His171 coordination. J. Inorg. Biochem. 2012, 108, 188–195.Search in Google Scholar

Vadon-Le Goff S.; Delaforge M.; Boucher J. L.; Janosik M.; Kraus J. P.; Mansuy D. Coordination chemistry of the heme in cystathionine beta-synthase: formation of iron(II)-isonitrile complexes. Biochem. Biophys. Res. Commun. 2001, 283, 487–492.Search in Google Scholar

Vreman H. J.; Wong R. J.; Kadotani T.; Stevenson D. K. Determination of carbon monoxide (CO) in rodent tissue: effect of heme administration and environmental CO exposure. Anal. Biochem. 2005, 341, 280–289.Search in Google Scholar

Weeks C. L.; Singh S.; Madzelan P.; Banerjee R.; Spiro T. G. Heme regulation of human cystathionine beta-synthase activity: insights from fluorescence and Raman spectroscopy. J. Am. Chem. Soc. 2009, 131, 12809–12816.Search in Google Scholar

Wolthers K. R.; Basran J.; Munro A. W.; Scrutton N. S. Molecular dissection of human methionine synthase reductase: determination of the flavin redox potentials in full-length enzyme and isolated flavin-binding domains. Biochemistry 2003, 42, 3911–3920.Search in Google Scholar

Wu L.; Wang R. Carbon monoxide: endogenous production, physiological functions, and pharmacological applications. Pharmacol. Rev. 2005, 57, 585–630.Search in Google Scholar

Yadav P. K.; Xie P.; Banerjee R. Allosteric communication between the PLP and heme sites in the H2S-generator human cystathionine β-synthase. J. Biol. Chem. 2012, 287, 37611–37620.Search in Google Scholar

Zhao W.; Zhang J.; Lu Y.; Wang R. The vasorelaxant effect of H(2)S as a novel endogenous gaseous K(ATP) channel opener. EMBO J. 2001, 20, 6008–6016.Search in Google Scholar

Received: 2013-6-14
Accepted: 2013-10-28
Published Online: 2014-01-08
Published in Print: 2013-12-01

©2013 by Walter de Gruyter Berlin Boston

Downloaded on 28.3.2024 from https://www.degruyter.com/document/doi/10.1515/irm-2013-0003/html
Scroll to top button