Substrate, Product, and Cofactor: The Extraordinarily Flexible Relationship Between the CDE Superfamily and Heme

Overview

Journal Arch Biochem Biophys

Publisher Elsevier

Specialties Biochemistry
Biophysics

Date 2015 Mar 18

PMID 25778630

Citations 22

Authors

Arianna I Celis

Jennifer L DuBois

Affiliations

Soon will be listed here.

Abstract

PFam Clan 0032, also known as the CDE superfamily, is a diverse group of at least 20 protein families sharing a common α,β-barrel domain. Of these, six different groups bind heme inside the barrel's interior, using it alternately as a cofactor, substrate, or product. Focusing on these six, an integrated picture of structure, sequence, taxonomy, and mechanism is presented here, detailing how a single structural motif might be able to mediate such an array of functions with one of nature's most important small molecules.

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References

Ahmad M, Roberts J, Hardiman E, Singh R, Eltis L, Bugg T . Identification of DypB from Rhodococcus jostii RHA1 as a lignin peroxidase. Biochemistry. 2011; 50(23):5096-107. DOI: 10.1021/bi101892z. View

Goblirsch B, Streit B, DuBois J, Wilmot C . Structural features promoting dioxygen production by Dechloromonas aromatica chlorite dismutase. J Biol Inorg Chem. 2010; 15(6):879-88. PMC: 2909366. DOI: 10.1007/s00775-010-0651-0. View

Reniere M, Ukpabi G, Harry S, Stec D, Krull R, Wright D . The IsdG-family of haem oxygenases degrades haem to a novel chromophore. Mol Microbiol. 2010; 75(6):1529-38. PMC: 3800195. DOI: 10.1111/j.1365-2958.2010.07076.x. View

Fetzner S, Steiner R . Cofactor-independent oxidases and oxygenases. Appl Microbiol Biotechnol. 2010; 86(3):791-804. DOI: 10.1007/s00253-010-2455-0. View

Sugano Y, Matsushima Y, Shoda M . Complete decolorization of the anthraquinone dye Reactive blue 5 by the concerted action of two peroxidases from Thanatephorus cucumeris Dec 1. Appl Microbiol Biotechnol. 2006; 73(4):862-71. DOI: 10.1007/s00253-006-0545-9. View

Celis A, Geeraerts Z, Ngmenterebo D, Machovina M, Kurker R, Rajakumar K . A dimeric chlorite dismutase exhibits O2-generating activity and acts as a chlorite antioxidant in Klebsiella pneumoniae MGH 78578. Biochemistry. 2014; 54(2):434-46. PMC: 4303309. DOI: 10.1021/bi501184c. View

Ruiz-Duenas F, Lundell T, Floudas D, Nagy L, Barrasa J, Hibbett D . Lignin-degrading peroxidases in Polyporales: an evolutionary survey based on 10 sequenced genomes. Mycologia. 2013; 105(6):1428-44. DOI: 10.3852/13-059. View

Smoot M, Ono K, Ruscheinski J, Wang P, Ideker T . Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2010; 27(3):431-2. PMC: 3031041. DOI: 10.1093/bioinformatics/btq675. View

Strittmatter E, Liers C, Ullrich R, Wachter S, Hofrichter M, Plattner D . First crystal structure of a fungal high-redox potential dye-decolorizing peroxidase: substrate interaction sites and long-range electron transfer. J Biol Chem. 2012; 288(6):4095-102. PMC: 3568178. DOI: 10.1074/jbc.M112.400176. View

10.

Sugano Y, Muramatsu R, Ichiyanagi A, Sato T, Shoda M . DyP, a unique dye-decolorizing peroxidase, represents a novel heme peroxidase family: ASP171 replaces the distal histidine of classical peroxidases. J Biol Chem. 2007; 282(50):36652-8. DOI: 10.1074/jbc.M706996200. View

11.

Linde D, Pogni R, Canellas M, Lucas F, Guallar V, Baratto M . Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study. Biochem J. 2014; 466(2):253-62. PMC: 4357238. DOI: 10.1042/BJ20141211. View

12.

Sigman J, Wang X, Lu Y . Coupled oxidation of heme by myoglobin is mediated by exogenous peroxide. J Am Chem Soc. 2001; 123(28):6945-6. DOI: 10.1021/ja015776u. View

13.

Dailey H, Septer A, Daugherty L, Thames D, Gerdes S, Stabb E . The Escherichia coli protein YfeX functions as a porphyrinogen oxidase, not a heme dechelatase. mBio. 2011; 2(6):e00248-11. PMC: 3215433. DOI: 10.1128/mBio.00248-11. View

14.

Veith A, Urich T, Seyfarth K, Protze J, Frazao C, Kletzin A . Substrate pathways and mechanisms of inhibition in the sulfur oxygenase reductase of acidianus ambivalens. Front Microbiol. 2011; 2:37. PMC: 3128934. DOI: 10.3389/fmicb.2011.00037. View

15.

Singh R, Grigg J, Qin W, Kadla J, Murphy M, Eltis L . Improved manganese-oxidizing activity of DypB, a peroxidase from a lignolytic bacterium. ACS Chem Biol. 2013; 8(4):700-6. PMC: 3631457. DOI: 10.1021/cb300608x. View

16.

KATTI S, Katz B, WYCKOFF H . Crystal structure of muconolactone isomerase at 3.3 A resolution. J Mol Biol. 1989; 205(3):557-71. DOI: 10.1016/0022-2836(89)90226-x. View

17.

Balaji Rao B, Hatzinger P, Bohlke J, Sturchio N, Andraski B, Eckardt F . Natural chlorate in the environment: application of a new IC-ESI/MS/MS method with a Cl¹⁸O₃-internal standard. Environ Sci Technol. 2010; 44(22):8429-34. DOI: 10.1021/es1024228. View

18.

Carra P, Colleran E . Methine-bridge specificity of the coupled oxidation of myoglobin and haemoglobin with ascorbate. Biochem J. 1970; 119(5):42P-43P. PMC: 1179513. DOI: 10.1042/bj1190042p. View

19.

Mayfield J, Hammer N, Kurker R, Chen T, Ojha S, Skaar E . The chlorite dismutase (HemQ) from Staphylococcus aureus has a redox-sensitive heme and is associated with the small colony variant phenotype. J Biol Chem. 2013; 288(32):23488-504. PMC: 5395028. DOI: 10.1074/jbc.M112.442335. View

20.

Strittmatter E, Serrer K, Liers C, Ullrich R, Hofrichter M, Piontek K . The toolbox of Auricularia auricula-judae dye-decolorizing peroxidase - Identification of three new potential substrate-interaction sites. Arch Biochem Biophys. 2014; 574:75-85. DOI: 10.1016/j.abb.2014.12.016. View