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Superoxide dismutases and superoxide reductases.

Sheng Y, Abreu IA, Cabelli DE, Maroney MJ, Miller AF, Teixeira M, Valentine JS - Chem. Rev. (2014)

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Affiliation: Department of Chemistry and Biochemistry, University of California Los Angeles , Los Angeles, California 90095, United States.

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SODs catalyze the disproportionationof superoxide to give O2 and H2O2, a reaction requiring one proton per superoxide reacted, but noexternal reductant (eq 7). 67 All of the SOR enzymes contain only iron, while the three typesof SODs are the nickel-containing SODs (NiSOD), the iron- or manganese-containingSODs (FeSOD and MnSOD), and the copper- and zinc-containing SODs (CuZnSOD).Although the structures and other properties of these four types ofmetalloenzymes are quite different, they all share several characteristics,including the ability to react rapidly and selectively with the smallanionic substrate O2... The first and most obviousof the similarities between these enzymes is that they all containredox-active metal ions at their active sites: Ni inNiSOD, Fe in FeSOD and SOR, Mn inMnSOD, and Cu in CuZnSOD... Another propertyshared by some but not all SODs is irreversible inactivation of theenzyme resulting from reaction of the reduced SOD with H2O2... This reaction, generally termed the peroxidative reaction,is the result of a Fenton-type reaction in which the reduced metalion at the active site reduces H2O2 to generatehydroxyl radical, which then reacts with amino acid residues nearby.Interestingly, eukaryotic CuZnSODs and most FeSODs react rapidly inthis fashion with H2O2, whereas MnSOD and prokaryoticCuZnSODs do not... These are difficult values for Niaq ions to achieve because water will both oxidize and reduceat potentials less extreme than Niaq... In fact,of the redox metal ions found in SODs, only nickel does not catalyzesuperoxide disproportionation in aqueous solution... Thislow reactivity with O2 is reminiscent of that of SORs (seesection 7) and contrasts with that of the mononuclearnonheme Fe sites of oxygenase enzymes, in which O2 reactsreadily with the Fe state of the enzyme once the co-substrateis bound (reviewed in refs... Earlywork on FeSOD found that small anions do not coordinate directly toFe even though they do coordinate directly to Fe... If a SOD is inactivated by H2O2, it is often claimed that the SOD must be an FeSOD or a CuZnSODand, if it is not inactivated by H2O2, thatit must be a MnSOD (or NiSOD)... This mechanismis most effective when proton transfer is coupled to electron transfer.Because this is the case for both FeSOD and MnSOD, both of these proteinshave the possibility of tuning the metal ion’s E° via modulation of the energy associated with proton uptake,that is, changing the pKa’s ofthe OH/H2O ligand in the reduced andoxidized states (Figure 16)... Fully functional humanCu,Zn-SOD1 is extraordinarilystable, melting at 92 °C and remaining folded in 8 M urea or1% SDS (reviewed in ref... Removal of the metal ions (E,E-SOD1) decreases the melting temperature to 54 °C, and reduction of the disulfide bond results in the leaststable form (E,E-SOD1), which melts at 42 °C... A more interesting hypothesisis that the lysine, upon detachmentof the glutamate, would acquire a position that allows it to stabilizethe hydroperoxide ligand, either directly or through water molecules,and would also facilitate the protonation of the hydroperoxo (by acidifyingthe water molecule)... As just mentioned, the distinct results foundfor different enzymes are inconclusive in this respect, or, as itso often occurs, the enzymes are particularly robust for those singleamino acid changes... The fact thatfour evolutionarily unrelated metalloenzymes arose to protect organismsagainst O2 toxicity, that is, NiSOD,Fe/MnSODs, CuZnSOD, and SORs, provides excellent examples both ofconvergent evolution and of nature’s ingenuity (in a Darwinianand a non teleological sense).

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Unrooted dendogram of 53 members of theFeSOD and MnSOD familywherein branches are colored as follows (clockwise from top left):blue for mitochondrial MnSODs, magenta for archaeal SODs, teal foractinobacterial SODs, pink for bacterial MnSODs, light green for cyanobacterialFeSODs, dark green for FeSODs of plants and green algae, red for FeSODsof protists, and orange for FeSODs of bacteria. Sequences were chosento represent diverse groups of organisms and different metal specificities.188c BLAST searches of the nonredundant databaseof the National Center for Biotechnology and Information (NCBI) wereused to identify additional SOD sequences from weakly representedgroups, and, in those cases in which sequences were very similar,only one exemplar was retained, the one for which the best informationon metal ion use was available. Where possible, for bacterial andarchaeal SODs especially, the identity of an SOD as Fe-dependent versusMn-dependent was sought in primary literature, and the means by whichits metal ion identity was determined is listed as “Anal”for direct analysis via atomic absorption or another spectroscopicmethod, or “H2O2” when it wasinferred on the basis of the SOD’s sensitivity or resistanceto inactivation by H2O2 and a reference is provided.Some Fe/MnSODs are included, but given that the motivation of thisexercise was to identify residues that correlate differentially withFe or Mn use, others are described via Table 4 instead. The tree was displayed and colored using the interactivetree of life server hosted by the European Molecular Biology Laboratory.400 The multiple sequence alignment upon whichit is based was generated using MUSCLE401 (in the “full” most stringent mode) for up to 16 interactions,as accessed via Phylogeny.fr hosted by the Centre National de la RechercheScientifique.402 The alignment was curatedusing Gblocks403 at the most stringentsetting (not allowing many contiguous nonconserved positions), andthe results were inspected visually via the Phylogeny.fr interface.The phylogenetic tree was constructed by PhyML using the approximatelikelihood-ratio test404 and using thesubstitution model of Jones, Taylor, and Thornton with default parameters,and gaps were removed from the alignment. The tree topology was confirmedwith COBALT via the National Center for Biotechnology Informationserver.405 The sequences are identifiedin the figure using the following abbreviations corresponding to thefollowing accession numbers: Afumig-Mn, Aspergillusfumigatus MnSOD (Eukaryota-mito) GI:18158811; Ahydro-Fe, Aeromonas hydrophila FeSOD(Gammaproteobacteria-Fe) GI:75530508; Anabae-Mn, Anabaena MnSOD (Cyanobacteria) GI:23200075 H2O2;406 Apernix-Mn/Fe, Aeropyrum pernix Mn/FeSOD (Crenarchaeota) GI:321159640;119 Athali-Fe, Arabidopsisthaliana FeSOD (Viridiplantae) GI:332659609; Athal-Mn, Arabidopsis thaliana MnSOD(Viridiplantae-mito) GI:15228407; Avine-Fe, Azotobacter vinelandii FeSOD (Gammaproteobacteria-Fe) GI:226720755 Anal.;407 Bthuri-Mn, Bacillusthuringiensis MnSOD (Firmicutes) GI:228830333; Cauran-Mn, Chloroflexus aurantiacus MnSOD (Chloroflexii) GI:31074373 Anal.;408 Cburne-Fe, Coxiella burnetii FeSOD (Gammaproteobacteria-Fe) GI:145002 H2O2;409 Cgluta-Mn, Corynebacteriumglutamicum MnSOD (Actinobacteria) GI:81783000; Cjejun-Fe, Campylobacter jejuni FeSOD(Epsilonproteobacteria) GI:218561849 H2O2;410 Creinh-Fe, Chlamydomonasreinhard FeSOD (Viridiplantae) GI:158280091; Dmelan-Mn, Drosophila melanogaster MnSOD (Eukaryota-mito) GI:7302882; Dradio-Mn, Deinococcus radiodurans MnSOD (Bacteria-Deinococ) GI:32363428; Ecoli-Fe, E. coli FeSOD (Gammaproteobacteria-Fe) GI:84028734 Anal;75a Ecoli-Mn, E.coli MnSOD (Gammaproteobacteria-Mn) GI:134659 Anal;74a,114c Ehist-Fe, Entamoeba histolytica FeSOD(protozoan-Eukaryota) GI:464774 H2O2;411 Ggallu-Mn, Gallusgallus MnSOD (Eukaryota-mito) GI:15419940; Hpylor-Fe, Helicobacter pylori FeSOD(Epsilonproteobacteria) GI:190016324;412 Hsap-Mn, Homo sapiens MnSOD (Eukaryota-mito) GI:24987871; Livano-Mn, Listeria ivanovii MnSOD(Firmicutes) GI:134666; Mbark-Fe, Methanosarcina barkeri FeSOD (Euryarchaeota) GI:499627762 Anal.;196d Methylo-Mn, Methylomonas MnSOD (Gammaproteobacteria-Mn) GI:95281 Anal;121 Mpalea-Fe, Marchantia paleacea FeSOD(Viridiplantae) GI:75243372; Msativ-Fe, Medicago sativa FeSOD (Viridiplantae) GI:75248782; Msmeg-Mn, Mycobacterium smegmatis MnSOD (Actinobacteria) GI:21264517 Anal;120 Mthermo-Fe, Methanobacteriumthermoauto FeSOD (Euryarchaeota) GI:23200500; Mtuber-Fe, Mycobacterium tuberculosis FeSOD (Actinobacteria) GI:809164 H2O2;413 Nmenin-Fe, Neisseriameningitidis FeSOD (Betaproteobacteria) GI:7226122; Naster-Mn, Nocardia asteroides MnSOD(Actinobacteria) GI:1711453; Nostoc-Fe, Nostoc PCC7120 FeSOD (Cyanobacteria) GI:17132032; Paeroph-Mn/Fe, Pyrobaculum aerophilum Mn/FeSOD (Crenarchaeota) GI:14917043;118 Pborya-Fe,: Plectonemaboryanum FeSOD (Cyanobacteria) GI:1711435 Anal;156b Pfalc-Fe, Plasmodiumfalciparum FeSOD (protozoan-Eukaryota) GI:74946757;414 Pfreud-FeMn, Propionibacteriumfreudenreichii (shermanii) Fe/MnSOD(Actinobacteria) GI:5542134 Anal.;113b Phalo-Fe, Pseudoalteromonas haloplanktis FeSOD (Gammaproteobacteria-Fe) GI:306440524; Pleiog-Fe, Photobacterium leiognathi FeSOD (Gammaproteobacteria-Fe) GI:134643 Anal;139 Poliv-Mn, Paralichthys olivaceus MnSOD (Eukaryota-mito) GI:134676; Poval-Fe, Pseudomonas ovalis FeSOD (Gammaproteobacteria-Fe) GI:12084342 Anal;114d Ppinas-Fe, Pinuspinaster FeSOD (Viridiplantae) GI:75223482; Scere-Mn, Saccharomyces cerevisiae MnSOD (Eukaryota-mito) GI:217035334; Ssolfa-Fe, Sulfolobus solfataricus FeSOD (Crenarchaeota) GI:14286093 Anal.;115,208 Synech-Fe, Synechocystis 6803 FeSOD (Cyanobacteria) GI:1653111; Taest-Mn, Triticum aestivum MnSOD (Viridiplantae-mito) GI:62131095; Taq-Mn, Thermus aquaticus MnSOD(Bacteria-Deinococ) GI:1711455; Tbruce-Fe, Trypanosoma brucei B2 FeSOD (protozoan-Eukaryota) GI:70834946 H2O2;415 Telong-Fe, Thermosynechococcus elongatus FeSOD (Cyanobacteria) GI:34810955; Tgondi-Fe, Toxoplasma gondii FeSOD(protozoan-Eukaryota) GI:122066229; Vcart-Fe, Volvox carteri FeSOD (Viridiplantae) GI:121077704; Vchol-Mn, Vibrio cholerae MnSOD(Gammaproteobacteria-Mn) GI:14039308 upregulation in absenceof Fe;416 Vungui-Fe, Vignaunguiculata FeSOD (Viridiplantae) GI:56554197 H2O2;417 Xcamp-Mn, Xanthomonas campestris MnSOD (Gammaproteobacteria-Mn) GI:76364224.
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fig18: Unrooted dendogram of 53 members of theFeSOD and MnSOD familywherein branches are colored as follows (clockwise from top left):blue for mitochondrial MnSODs, magenta for archaeal SODs, teal foractinobacterial SODs, pink for bacterial MnSODs, light green for cyanobacterialFeSODs, dark green for FeSODs of plants and green algae, red for FeSODsof protists, and orange for FeSODs of bacteria. Sequences were chosento represent diverse groups of organisms and different metal specificities.188c BLAST searches of the nonredundant databaseof the National Center for Biotechnology and Information (NCBI) wereused to identify additional SOD sequences from weakly representedgroups, and, in those cases in which sequences were very similar,only one exemplar was retained, the one for which the best informationon metal ion use was available. Where possible, for bacterial andarchaeal SODs especially, the identity of an SOD as Fe-dependent versusMn-dependent was sought in primary literature, and the means by whichits metal ion identity was determined is listed as “Anal”for direct analysis via atomic absorption or another spectroscopicmethod, or “H2O2” when it wasinferred on the basis of the SOD’s sensitivity or resistanceto inactivation by H2O2 and a reference is provided.Some Fe/MnSODs are included, but given that the motivation of thisexercise was to identify residues that correlate differentially withFe or Mn use, others are described via Table 4 instead. The tree was displayed and colored using the interactivetree of life server hosted by the European Molecular Biology Laboratory.400 The multiple sequence alignment upon whichit is based was generated using MUSCLE401 (in the “full” most stringent mode) for up to 16 interactions,as accessed via Phylogeny.fr hosted by the Centre National de la RechercheScientifique.402 The alignment was curatedusing Gblocks403 at the most stringentsetting (not allowing many contiguous nonconserved positions), andthe results were inspected visually via the Phylogeny.fr interface.The phylogenetic tree was constructed by PhyML using the approximatelikelihood-ratio test404 and using thesubstitution model of Jones, Taylor, and Thornton with default parameters,and gaps were removed from the alignment. The tree topology was confirmedwith COBALT via the National Center for Biotechnology Informationserver.405 The sequences are identifiedin the figure using the following abbreviations corresponding to thefollowing accession numbers: Afumig-Mn, Aspergillusfumigatus MnSOD (Eukaryota-mito) GI:18158811; Ahydro-Fe, Aeromonas hydrophila FeSOD(Gammaproteobacteria-Fe) GI:75530508; Anabae-Mn, Anabaena MnSOD (Cyanobacteria) GI:23200075 H2O2;406 Apernix-Mn/Fe, Aeropyrum pernix Mn/FeSOD (Crenarchaeota) GI:321159640;119 Athali-Fe, Arabidopsisthaliana FeSOD (Viridiplantae) GI:332659609; Athal-Mn, Arabidopsis thaliana MnSOD(Viridiplantae-mito) GI:15228407; Avine-Fe, Azotobacter vinelandii FeSOD (Gammaproteobacteria-Fe) GI:226720755 Anal.;407 Bthuri-Mn, Bacillusthuringiensis MnSOD (Firmicutes) GI:228830333; Cauran-Mn, Chloroflexus aurantiacus MnSOD (Chloroflexii) GI:31074373 Anal.;408 Cburne-Fe, Coxiella burnetii FeSOD (Gammaproteobacteria-Fe) GI:145002 H2O2;409 Cgluta-Mn, Corynebacteriumglutamicum MnSOD (Actinobacteria) GI:81783000; Cjejun-Fe, Campylobacter jejuni FeSOD(Epsilonproteobacteria) GI:218561849 H2O2;410 Creinh-Fe, Chlamydomonasreinhard FeSOD (Viridiplantae) GI:158280091; Dmelan-Mn, Drosophila melanogaster MnSOD (Eukaryota-mito) GI:7302882; Dradio-Mn, Deinococcus radiodurans MnSOD (Bacteria-Deinococ) GI:32363428; Ecoli-Fe, E. coli FeSOD (Gammaproteobacteria-Fe) GI:84028734 Anal;75a Ecoli-Mn, E.coli MnSOD (Gammaproteobacteria-Mn) GI:134659 Anal;74a,114c Ehist-Fe, Entamoeba histolytica FeSOD(protozoan-Eukaryota) GI:464774 H2O2;411 Ggallu-Mn, Gallusgallus MnSOD (Eukaryota-mito) GI:15419940; Hpylor-Fe, Helicobacter pylori FeSOD(Epsilonproteobacteria) GI:190016324;412 Hsap-Mn, Homo sapiens MnSOD (Eukaryota-mito) GI:24987871; Livano-Mn, Listeria ivanovii MnSOD(Firmicutes) GI:134666; Mbark-Fe, Methanosarcina barkeri FeSOD (Euryarchaeota) GI:499627762 Anal.;196d Methylo-Mn, Methylomonas MnSOD (Gammaproteobacteria-Mn) GI:95281 Anal;121 Mpalea-Fe, Marchantia paleacea FeSOD(Viridiplantae) GI:75243372; Msativ-Fe, Medicago sativa FeSOD (Viridiplantae) GI:75248782; Msmeg-Mn, Mycobacterium smegmatis MnSOD (Actinobacteria) GI:21264517 Anal;120 Mthermo-Fe, Methanobacteriumthermoauto FeSOD (Euryarchaeota) GI:23200500; Mtuber-Fe, Mycobacterium tuberculosis FeSOD (Actinobacteria) GI:809164 H2O2;413 Nmenin-Fe, Neisseriameningitidis FeSOD (Betaproteobacteria) GI:7226122; Naster-Mn, Nocardia asteroides MnSOD(Actinobacteria) GI:1711453; Nostoc-Fe, Nostoc PCC7120 FeSOD (Cyanobacteria) GI:17132032; Paeroph-Mn/Fe, Pyrobaculum aerophilum Mn/FeSOD (Crenarchaeota) GI:14917043;118 Pborya-Fe,: Plectonemaboryanum FeSOD (Cyanobacteria) GI:1711435 Anal;156b Pfalc-Fe, Plasmodiumfalciparum FeSOD (protozoan-Eukaryota) GI:74946757;414 Pfreud-FeMn, Propionibacteriumfreudenreichii (shermanii) Fe/MnSOD(Actinobacteria) GI:5542134 Anal.;113b Phalo-Fe, Pseudoalteromonas haloplanktis FeSOD (Gammaproteobacteria-Fe) GI:306440524; Pleiog-Fe, Photobacterium leiognathi FeSOD (Gammaproteobacteria-Fe) GI:134643 Anal;139 Poliv-Mn, Paralichthys olivaceus MnSOD (Eukaryota-mito) GI:134676; Poval-Fe, Pseudomonas ovalis FeSOD (Gammaproteobacteria-Fe) GI:12084342 Anal;114d Ppinas-Fe, Pinuspinaster FeSOD (Viridiplantae) GI:75223482; Scere-Mn, Saccharomyces cerevisiae MnSOD (Eukaryota-mito) GI:217035334; Ssolfa-Fe, Sulfolobus solfataricus FeSOD (Crenarchaeota) GI:14286093 Anal.;115,208 Synech-Fe, Synechocystis 6803 FeSOD (Cyanobacteria) GI:1653111; Taest-Mn, Triticum aestivum MnSOD (Viridiplantae-mito) GI:62131095; Taq-Mn, Thermus aquaticus MnSOD(Bacteria-Deinococ) GI:1711455; Tbruce-Fe, Trypanosoma brucei B2 FeSOD (protozoan-Eukaryota) GI:70834946 H2O2;415 Telong-Fe, Thermosynechococcus elongatus FeSOD (Cyanobacteria) GI:34810955; Tgondi-Fe, Toxoplasma gondii FeSOD(protozoan-Eukaryota) GI:122066229; Vcart-Fe, Volvox carteri FeSOD (Viridiplantae) GI:121077704; Vchol-Mn, Vibrio cholerae MnSOD(Gammaproteobacteria-Mn) GI:14039308 upregulation in absenceof Fe;416 Vungui-Fe, Vignaunguiculata FeSOD (Viridiplantae) GI:56554197 H2O2;417 Xcamp-Mn, Xanthomonas campestris MnSOD (Gammaproteobacteria-Mn) GI:76364224.

Mentions: The sections that followdescribe how amino acid sequence similarities among Fe- and/or MnSODsare remarkably consistent with what is known about the evolution ofeukaryotic cells as well as the major branches of the tree of life.Mitochondrial MnSOD can be traced back to the archaeal origin of eukaryoticcells, chloroplast FeSOD to cyanobacterial origin and protist FeSODto bacterial origin (of possibly more than one type, and possiblyvia lateral gene transfer). The conservation of SODs across the domainsof life indicates that FeSODs and MnSODs existed as distinct typesevolving independently before the emergence of eukaryotes, becausethese two clusters separately (Figure 18).Distinct FeSODs and MnSODs appear to have arisen even before divergenceof major branches of bacteria, or moved among branches by lateralgene transfer.188a,194 However, FeSODs remain the mostwidely dispersed, consistent with a very early origin.195


Superoxide dismutases and superoxide reductases.

Sheng Y, Abreu IA, Cabelli DE, Maroney MJ, Miller AF, Teixeira M, Valentine JS - Chem. Rev. (2014)

Unrooted dendogram of 53 members of theFeSOD and MnSOD familywherein branches are colored as follows (clockwise from top left):blue for mitochondrial MnSODs, magenta for archaeal SODs, teal foractinobacterial SODs, pink for bacterial MnSODs, light green for cyanobacterialFeSODs, dark green for FeSODs of plants and green algae, red for FeSODsof protists, and orange for FeSODs of bacteria. Sequences were chosento represent diverse groups of organisms and different metal specificities.188c BLAST searches of the nonredundant databaseof the National Center for Biotechnology and Information (NCBI) wereused to identify additional SOD sequences from weakly representedgroups, and, in those cases in which sequences were very similar,only one exemplar was retained, the one for which the best informationon metal ion use was available. Where possible, for bacterial andarchaeal SODs especially, the identity of an SOD as Fe-dependent versusMn-dependent was sought in primary literature, and the means by whichits metal ion identity was determined is listed as “Anal”for direct analysis via atomic absorption or another spectroscopicmethod, or “H2O2” when it wasinferred on the basis of the SOD’s sensitivity or resistanceto inactivation by H2O2 and a reference is provided.Some Fe/MnSODs are included, but given that the motivation of thisexercise was to identify residues that correlate differentially withFe or Mn use, others are described via Table 4 instead. The tree was displayed and colored using the interactivetree of life server hosted by the European Molecular Biology Laboratory.400 The multiple sequence alignment upon whichit is based was generated using MUSCLE401 (in the “full” most stringent mode) for up to 16 interactions,as accessed via Phylogeny.fr hosted by the Centre National de la RechercheScientifique.402 The alignment was curatedusing Gblocks403 at the most stringentsetting (not allowing many contiguous nonconserved positions), andthe results were inspected visually via the Phylogeny.fr interface.The phylogenetic tree was constructed by PhyML using the approximatelikelihood-ratio test404 and using thesubstitution model of Jones, Taylor, and Thornton with default parameters,and gaps were removed from the alignment. The tree topology was confirmedwith COBALT via the National Center for Biotechnology Informationserver.405 The sequences are identifiedin the figure using the following abbreviations corresponding to thefollowing accession numbers: Afumig-Mn, Aspergillusfumigatus MnSOD (Eukaryota-mito) GI:18158811; Ahydro-Fe, Aeromonas hydrophila FeSOD(Gammaproteobacteria-Fe) GI:75530508; Anabae-Mn, Anabaena MnSOD (Cyanobacteria) GI:23200075 H2O2;406 Apernix-Mn/Fe, Aeropyrum pernix Mn/FeSOD (Crenarchaeota) GI:321159640;119 Athali-Fe, Arabidopsisthaliana FeSOD (Viridiplantae) GI:332659609; Athal-Mn, Arabidopsis thaliana MnSOD(Viridiplantae-mito) GI:15228407; Avine-Fe, Azotobacter vinelandii FeSOD (Gammaproteobacteria-Fe) GI:226720755 Anal.;407 Bthuri-Mn, Bacillusthuringiensis MnSOD (Firmicutes) GI:228830333; Cauran-Mn, Chloroflexus aurantiacus MnSOD (Chloroflexii) GI:31074373 Anal.;408 Cburne-Fe, Coxiella burnetii FeSOD (Gammaproteobacteria-Fe) GI:145002 H2O2;409 Cgluta-Mn, Corynebacteriumglutamicum MnSOD (Actinobacteria) GI:81783000; Cjejun-Fe, Campylobacter jejuni FeSOD(Epsilonproteobacteria) GI:218561849 H2O2;410 Creinh-Fe, Chlamydomonasreinhard FeSOD (Viridiplantae) GI:158280091; Dmelan-Mn, Drosophila melanogaster MnSOD (Eukaryota-mito) GI:7302882; Dradio-Mn, Deinococcus radiodurans MnSOD (Bacteria-Deinococ) GI:32363428; Ecoli-Fe, E. coli FeSOD (Gammaproteobacteria-Fe) GI:84028734 Anal;75a Ecoli-Mn, E.coli MnSOD (Gammaproteobacteria-Mn) GI:134659 Anal;74a,114c Ehist-Fe, Entamoeba histolytica FeSOD(protozoan-Eukaryota) GI:464774 H2O2;411 Ggallu-Mn, Gallusgallus MnSOD (Eukaryota-mito) GI:15419940; Hpylor-Fe, Helicobacter pylori FeSOD(Epsilonproteobacteria) GI:190016324;412 Hsap-Mn, Homo sapiens MnSOD (Eukaryota-mito) GI:24987871; Livano-Mn, Listeria ivanovii MnSOD(Firmicutes) GI:134666; Mbark-Fe, Methanosarcina barkeri FeSOD (Euryarchaeota) GI:499627762 Anal.;196d Methylo-Mn, Methylomonas MnSOD (Gammaproteobacteria-Mn) GI:95281 Anal;121 Mpalea-Fe, Marchantia paleacea FeSOD(Viridiplantae) GI:75243372; Msativ-Fe, Medicago sativa FeSOD (Viridiplantae) GI:75248782; Msmeg-Mn, Mycobacterium smegmatis MnSOD (Actinobacteria) GI:21264517 Anal;120 Mthermo-Fe, Methanobacteriumthermoauto FeSOD (Euryarchaeota) GI:23200500; Mtuber-Fe, Mycobacterium tuberculosis FeSOD (Actinobacteria) GI:809164 H2O2;413 Nmenin-Fe, Neisseriameningitidis FeSOD (Betaproteobacteria) GI:7226122; Naster-Mn, Nocardia asteroides MnSOD(Actinobacteria) GI:1711453; Nostoc-Fe, Nostoc PCC7120 FeSOD (Cyanobacteria) GI:17132032; Paeroph-Mn/Fe, Pyrobaculum aerophilum Mn/FeSOD (Crenarchaeota) GI:14917043;118 Pborya-Fe,: Plectonemaboryanum FeSOD (Cyanobacteria) GI:1711435 Anal;156b Pfalc-Fe, Plasmodiumfalciparum FeSOD (protozoan-Eukaryota) GI:74946757;414 Pfreud-FeMn, Propionibacteriumfreudenreichii (shermanii) Fe/MnSOD(Actinobacteria) GI:5542134 Anal.;113b Phalo-Fe, Pseudoalteromonas haloplanktis FeSOD (Gammaproteobacteria-Fe) GI:306440524; Pleiog-Fe, Photobacterium leiognathi FeSOD (Gammaproteobacteria-Fe) GI:134643 Anal;139 Poliv-Mn, Paralichthys olivaceus MnSOD (Eukaryota-mito) GI:134676; Poval-Fe, Pseudomonas ovalis FeSOD (Gammaproteobacteria-Fe) GI:12084342 Anal;114d Ppinas-Fe, Pinuspinaster FeSOD (Viridiplantae) GI:75223482; Scere-Mn, Saccharomyces cerevisiae MnSOD (Eukaryota-mito) GI:217035334; Ssolfa-Fe, Sulfolobus solfataricus FeSOD (Crenarchaeota) GI:14286093 Anal.;115,208 Synech-Fe, Synechocystis 6803 FeSOD (Cyanobacteria) GI:1653111; Taest-Mn, Triticum aestivum MnSOD (Viridiplantae-mito) GI:62131095; Taq-Mn, Thermus aquaticus MnSOD(Bacteria-Deinococ) GI:1711455; Tbruce-Fe, Trypanosoma brucei B2 FeSOD (protozoan-Eukaryota) GI:70834946 H2O2;415 Telong-Fe, Thermosynechococcus elongatus FeSOD (Cyanobacteria) GI:34810955; Tgondi-Fe, Toxoplasma gondii FeSOD(protozoan-Eukaryota) GI:122066229; Vcart-Fe, Volvox carteri FeSOD (Viridiplantae) GI:121077704; Vchol-Mn, Vibrio cholerae MnSOD(Gammaproteobacteria-Mn) GI:14039308 upregulation in absenceof Fe;416 Vungui-Fe, Vignaunguiculata FeSOD (Viridiplantae) GI:56554197 H2O2;417 Xcamp-Mn, Xanthomonas campestris MnSOD (Gammaproteobacteria-Mn) GI:76364224.
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fig18: Unrooted dendogram of 53 members of theFeSOD and MnSOD familywherein branches are colored as follows (clockwise from top left):blue for mitochondrial MnSODs, magenta for archaeal SODs, teal foractinobacterial SODs, pink for bacterial MnSODs, light green for cyanobacterialFeSODs, dark green for FeSODs of plants and green algae, red for FeSODsof protists, and orange for FeSODs of bacteria. Sequences were chosento represent diverse groups of organisms and different metal specificities.188c BLAST searches of the nonredundant databaseof the National Center for Biotechnology and Information (NCBI) wereused to identify additional SOD sequences from weakly representedgroups, and, in those cases in which sequences were very similar,only one exemplar was retained, the one for which the best informationon metal ion use was available. Where possible, for bacterial andarchaeal SODs especially, the identity of an SOD as Fe-dependent versusMn-dependent was sought in primary literature, and the means by whichits metal ion identity was determined is listed as “Anal”for direct analysis via atomic absorption or another spectroscopicmethod, or “H2O2” when it wasinferred on the basis of the SOD’s sensitivity or resistanceto inactivation by H2O2 and a reference is provided.Some Fe/MnSODs are included, but given that the motivation of thisexercise was to identify residues that correlate differentially withFe or Mn use, others are described via Table 4 instead. The tree was displayed and colored using the interactivetree of life server hosted by the European Molecular Biology Laboratory.400 The multiple sequence alignment upon whichit is based was generated using MUSCLE401 (in the “full” most stringent mode) for up to 16 interactions,as accessed via Phylogeny.fr hosted by the Centre National de la RechercheScientifique.402 The alignment was curatedusing Gblocks403 at the most stringentsetting (not allowing many contiguous nonconserved positions), andthe results were inspected visually via the Phylogeny.fr interface.The phylogenetic tree was constructed by PhyML using the approximatelikelihood-ratio test404 and using thesubstitution model of Jones, Taylor, and Thornton with default parameters,and gaps were removed from the alignment. The tree topology was confirmedwith COBALT via the National Center for Biotechnology Informationserver.405 The sequences are identifiedin the figure using the following abbreviations corresponding to thefollowing accession numbers: Afumig-Mn, Aspergillusfumigatus MnSOD (Eukaryota-mito) GI:18158811; Ahydro-Fe, Aeromonas hydrophila FeSOD(Gammaproteobacteria-Fe) GI:75530508; Anabae-Mn, Anabaena MnSOD (Cyanobacteria) GI:23200075 H2O2;406 Apernix-Mn/Fe, Aeropyrum pernix Mn/FeSOD (Crenarchaeota) GI:321159640;119 Athali-Fe, Arabidopsisthaliana FeSOD (Viridiplantae) GI:332659609; Athal-Mn, Arabidopsis thaliana MnSOD(Viridiplantae-mito) GI:15228407; Avine-Fe, Azotobacter vinelandii FeSOD (Gammaproteobacteria-Fe) GI:226720755 Anal.;407 Bthuri-Mn, Bacillusthuringiensis MnSOD (Firmicutes) GI:228830333; Cauran-Mn, Chloroflexus aurantiacus MnSOD (Chloroflexii) GI:31074373 Anal.;408 Cburne-Fe, Coxiella burnetii FeSOD (Gammaproteobacteria-Fe) GI:145002 H2O2;409 Cgluta-Mn, Corynebacteriumglutamicum MnSOD (Actinobacteria) GI:81783000; Cjejun-Fe, Campylobacter jejuni FeSOD(Epsilonproteobacteria) GI:218561849 H2O2;410 Creinh-Fe, Chlamydomonasreinhard FeSOD (Viridiplantae) GI:158280091; Dmelan-Mn, Drosophila melanogaster MnSOD (Eukaryota-mito) GI:7302882; Dradio-Mn, Deinococcus radiodurans MnSOD (Bacteria-Deinococ) GI:32363428; Ecoli-Fe, E. coli FeSOD (Gammaproteobacteria-Fe) GI:84028734 Anal;75a Ecoli-Mn, E.coli MnSOD (Gammaproteobacteria-Mn) GI:134659 Anal;74a,114c Ehist-Fe, Entamoeba histolytica FeSOD(protozoan-Eukaryota) GI:464774 H2O2;411 Ggallu-Mn, Gallusgallus MnSOD (Eukaryota-mito) GI:15419940; Hpylor-Fe, Helicobacter pylori FeSOD(Epsilonproteobacteria) GI:190016324;412 Hsap-Mn, Homo sapiens MnSOD (Eukaryota-mito) GI:24987871; Livano-Mn, Listeria ivanovii MnSOD(Firmicutes) GI:134666; Mbark-Fe, Methanosarcina barkeri FeSOD (Euryarchaeota) GI:499627762 Anal.;196d Methylo-Mn, Methylomonas MnSOD (Gammaproteobacteria-Mn) GI:95281 Anal;121 Mpalea-Fe, Marchantia paleacea FeSOD(Viridiplantae) GI:75243372; Msativ-Fe, Medicago sativa FeSOD (Viridiplantae) GI:75248782; Msmeg-Mn, Mycobacterium smegmatis MnSOD (Actinobacteria) GI:21264517 Anal;120 Mthermo-Fe, Methanobacteriumthermoauto FeSOD (Euryarchaeota) GI:23200500; Mtuber-Fe, Mycobacterium tuberculosis FeSOD (Actinobacteria) GI:809164 H2O2;413 Nmenin-Fe, Neisseriameningitidis FeSOD (Betaproteobacteria) GI:7226122; Naster-Mn, Nocardia asteroides MnSOD(Actinobacteria) GI:1711453; Nostoc-Fe, Nostoc PCC7120 FeSOD (Cyanobacteria) GI:17132032; Paeroph-Mn/Fe, Pyrobaculum aerophilum Mn/FeSOD (Crenarchaeota) GI:14917043;118 Pborya-Fe,: Plectonemaboryanum FeSOD (Cyanobacteria) GI:1711435 Anal;156b Pfalc-Fe, Plasmodiumfalciparum FeSOD (protozoan-Eukaryota) GI:74946757;414 Pfreud-FeMn, Propionibacteriumfreudenreichii (shermanii) Fe/MnSOD(Actinobacteria) GI:5542134 Anal.;113b Phalo-Fe, Pseudoalteromonas haloplanktis FeSOD (Gammaproteobacteria-Fe) GI:306440524; Pleiog-Fe, Photobacterium leiognathi FeSOD (Gammaproteobacteria-Fe) GI:134643 Anal;139 Poliv-Mn, Paralichthys olivaceus MnSOD (Eukaryota-mito) GI:134676; Poval-Fe, Pseudomonas ovalis FeSOD (Gammaproteobacteria-Fe) GI:12084342 Anal;114d Ppinas-Fe, Pinuspinaster FeSOD (Viridiplantae) GI:75223482; Scere-Mn, Saccharomyces cerevisiae MnSOD (Eukaryota-mito) GI:217035334; Ssolfa-Fe, Sulfolobus solfataricus FeSOD (Crenarchaeota) GI:14286093 Anal.;115,208 Synech-Fe, Synechocystis 6803 FeSOD (Cyanobacteria) GI:1653111; Taest-Mn, Triticum aestivum MnSOD (Viridiplantae-mito) GI:62131095; Taq-Mn, Thermus aquaticus MnSOD(Bacteria-Deinococ) GI:1711455; Tbruce-Fe, Trypanosoma brucei B2 FeSOD (protozoan-Eukaryota) GI:70834946 H2O2;415 Telong-Fe, Thermosynechococcus elongatus FeSOD (Cyanobacteria) GI:34810955; Tgondi-Fe, Toxoplasma gondii FeSOD(protozoan-Eukaryota) GI:122066229; Vcart-Fe, Volvox carteri FeSOD (Viridiplantae) GI:121077704; Vchol-Mn, Vibrio cholerae MnSOD(Gammaproteobacteria-Mn) GI:14039308 upregulation in absenceof Fe;416 Vungui-Fe, Vignaunguiculata FeSOD (Viridiplantae) GI:56554197 H2O2;417 Xcamp-Mn, Xanthomonas campestris MnSOD (Gammaproteobacteria-Mn) GI:76364224.
Mentions: The sections that followdescribe how amino acid sequence similarities among Fe- and/or MnSODsare remarkably consistent with what is known about the evolution ofeukaryotic cells as well as the major branches of the tree of life.Mitochondrial MnSOD can be traced back to the archaeal origin of eukaryoticcells, chloroplast FeSOD to cyanobacterial origin and protist FeSODto bacterial origin (of possibly more than one type, and possiblyvia lateral gene transfer). The conservation of SODs across the domainsof life indicates that FeSODs and MnSODs existed as distinct typesevolving independently before the emergence of eukaryotes, becausethese two clusters separately (Figure 18).Distinct FeSODs and MnSODs appear to have arisen even before divergenceof major branches of bacteria, or moved among branches by lateralgene transfer.188a,194 However, FeSODs remain the mostwidely dispersed, consistent with a very early origin.195

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Affiliation: Department of Chemistry and Biochemistry, University of California Los Angeles , Los Angeles, California 90095, United States.

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SODs catalyze the disproportionationof superoxide to give O2 and H2O2, a reaction requiring one proton per superoxide reacted, but noexternal reductant (eq 7). 67 All of the SOR enzymes contain only iron, while the three typesof SODs are the nickel-containing SODs (NiSOD), the iron- or manganese-containingSODs (FeSOD and MnSOD), and the copper- and zinc-containing SODs (CuZnSOD).Although the structures and other properties of these four types ofmetalloenzymes are quite different, they all share several characteristics,including the ability to react rapidly and selectively with the smallanionic substrate O2... The first and most obviousof the similarities between these enzymes is that they all containredox-active metal ions at their active sites: Ni inNiSOD, Fe in FeSOD and SOR, Mn inMnSOD, and Cu in CuZnSOD... Another propertyshared by some but not all SODs is irreversible inactivation of theenzyme resulting from reaction of the reduced SOD with H2O2... This reaction, generally termed the peroxidative reaction,is the result of a Fenton-type reaction in which the reduced metalion at the active site reduces H2O2 to generatehydroxyl radical, which then reacts with amino acid residues nearby.Interestingly, eukaryotic CuZnSODs and most FeSODs react rapidly inthis fashion with H2O2, whereas MnSOD and prokaryoticCuZnSODs do not... These are difficult values for Niaq ions to achieve because water will both oxidize and reduceat potentials less extreme than Niaq... In fact,of the redox metal ions found in SODs, only nickel does not catalyzesuperoxide disproportionation in aqueous solution... Thislow reactivity with O2 is reminiscent of that of SORs (seesection 7) and contrasts with that of the mononuclearnonheme Fe sites of oxygenase enzymes, in which O2 reactsreadily with the Fe state of the enzyme once the co-substrateis bound (reviewed in refs... Earlywork on FeSOD found that small anions do not coordinate directly toFe even though they do coordinate directly to Fe... If a SOD is inactivated by H2O2, it is often claimed that the SOD must be an FeSOD or a CuZnSODand, if it is not inactivated by H2O2, thatit must be a MnSOD (or NiSOD)... This mechanismis most effective when proton transfer is coupled to electron transfer.Because this is the case for both FeSOD and MnSOD, both of these proteinshave the possibility of tuning the metal ion’s E° via modulation of the energy associated with proton uptake,that is, changing the pKa’s ofthe OH/H2O ligand in the reduced andoxidized states (Figure 16)... Fully functional humanCu,Zn-SOD1 is extraordinarilystable, melting at 92 °C and remaining folded in 8 M urea or1% SDS (reviewed in ref... Removal of the metal ions (E,E-SOD1) decreases the melting temperature to 54 °C, and reduction of the disulfide bond results in the leaststable form (E,E-SOD1), which melts at 42 °C... A more interesting hypothesisis that the lysine, upon detachmentof the glutamate, would acquire a position that allows it to stabilizethe hydroperoxide ligand, either directly or through water molecules,and would also facilitate the protonation of the hydroperoxo (by acidifyingthe water molecule)... As just mentioned, the distinct results foundfor different enzymes are inconclusive in this respect, or, as itso often occurs, the enzymes are particularly robust for those singleamino acid changes... The fact thatfour evolutionarily unrelated metalloenzymes arose to protect organismsagainst O2 toxicity, that is, NiSOD,Fe/MnSODs, CuZnSOD, and SORs, provides excellent examples both ofconvergent evolution and of nature’s ingenuity (in a Darwinianand a non teleological sense).

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