PDBsum entry 1isc

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Oxidoreductase(superoxide acceptor) PDB id
Protein chains
192 a.a. *
AZI ×2
_FE ×2
Waters ×272
* Residue conservation analysis
PDB id:
Name: Oxidoreductase(superoxide acceptor)
Title: Structure-function in e. Coli iron superoxide dismutase: comparisons with the manganese enzyme from t. Thermophilus
Structure: Iron(iii) superoxide dismutase. Chain: a, b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562.
Biol. unit: Dimer (from PQS)
1.80Å     R-factor:   0.185    
Authors: M.S.Lah,M.Dixon,K.A.Pattridge,W.C.Stallings,J.A.Fee, M.L.Ludwig
Key ref:
M.S.Lah et al. (1995). Structure-function in Escherichia coli iron superoxide dismutase: comparisons with the manganese enzyme from Thermus thermophilus. Biochemistry, 34, 1646-1660. PubMed id: 7849024 DOI: 10.1021/bi00005a021
12-Jul-94     Release date:   30-Sep-94    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0AGD3  (SODF_ECOLI) -  Superoxide dismutase [Fe]
193 a.a.
192 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     oxidoreductase activity     4 terms  


DOI no: 10.1021/bi00005a021 Biochemistry 34:1646-1660 (1995)
PubMed id: 7849024  
Structure-function in Escherichia coli iron superoxide dismutase: comparisons with the manganese enzyme from Thermus thermophilus.
M.S.Lah, M.M.Dixon, K.A.Pattridge, W.C.Stallings, J.A.Fee, M.L.Ludwig.
The crystal structure of dimeric Fe(III) superoxide dismutase (SOD) from Escherichia coli (3006 protein atoms, 2 irons, and 281 solvents) has been refined to an R of 0.184 using all observed data between 40.0 and 1.85 A (34,879 reflections). Features of this structure are compared with the refined structure of MnSOD from Thermus thermophilus. The coordination geometry at the Fe site is distorted trigonal bipyramidal, with axial ligands His26 and solvent (proposed to be OH-), and in-plane ligands His73, Asp156, and His160. Reduction of crystals to the Fe(II) state does not result in significant changes in metal-ligand geometry (R = 0.188 for data between 40.0 and 1.80 A). The arrangement of iron ligands in Fe(II) and Fe(III)SOD closely matches the Mn coordination found in MnSOD from T. thermophilus [Ludwig, M.L., Metzger, A.L., Pattridge, K.A., & Stallings, W.C. (1991) J. Mol. Biol. 219, 335-358]. Structures of the Fe(III) azide (40.0-1.8 A, R = 0.186) and Mn(III) azide (20.0-1.8 A, R = 0.179) complexes, reported here, reveal azide bound as a sixth ligand with distorted octahedral geometry at the metal; the in-plane ligand-Fe-ligand and ligand-Mn-ligand angles change by 20-30 degrees to coordinate azide as a sixth ligand. However, the positions of the distal azide nitrogens are different in the FeSOD and MnSOD complexes. The geometries of the Fe(III), Fe(II), and Fe(III)-azide species suggest a reaction mechanism for superoxide dismutation in which the metal alternates between five- and six-coordination. A reaction scheme in which the ligated solvent acts as a proton acceptor in the first half-reaction [formation of Fe(II) and oxygen] is consistent with the pH dependence of the kinetic parameters and spectroscopic properties of Fe superoxide dismutase.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21182595 T.Nakamura, K.Torikai, K.Uegaki, J.Morita, K.Machida, A.Suzuki, and Y.Kawata (2011).
Crystal structure of the cambialistic superoxide dismutase from Aeropyrum pernix K1--insights into the enzyme mechanism and stability.
  FEBS J, 278, 598-609.
PDB codes: 3ak1 3ak2 3ak3
20603674 H.Dong (2010).
A computational study towards understanding the mechanism of phosphodiester cleavage by two mononuclear Zn(II) complexes.
  Phys Chem Chem Phys, 12, 10434-10443.  
19707802 H.I.Lee, J.W.Lee, T.C.Yang, S.O.Kang, and B.M.Hoffman (2010).
ENDOR and ESEEM investigation of the Ni-containing superoxide dismutase.
  J Biol Inorg Chem, 15, 175-182.  
20972560 H.Xiang, G.Pan, C.R.Vossbrinck, R.Zhang, J.Xu, T.Li, Z.Zhou, C.Lu, and Z.Xiang (2010).
A Tandem Duplication of Manganese Superoxide Dismutase in Nosema bombycis and Its Evolutionary Origins.
  J Mol Evol, 71, 401-414.  
19699328 J.W.Whittaker (2010).
Metal uptake by manganese superoxide dismutase.
  Biochim Biophys Acta, 1804, 298-307.  
20333421 K.C.Ryan, O.E.Johnson, D.E.Cabelli, T.C.Brunold, and M.J.Maroney (2010).
Nickel superoxide dismutase: structural and functional roles of Cys2 and Cys6.
  J Biol Inorg Chem, 15, 795-807.  
20657939 Q.Li, T.A.van den Berg, B.L.Feringa, and G.Roelfes (2010).
Mononuclear Fe(II)-N4Py complexes in oxidative DNA cleavage: structure, activity and mechanism.
  Dalton Trans, 39, 8012-8021.  
  19886398 A.Valdivia, S.Pérez-Alvarez, J.D.Aroca-Aguilar, I.Ikuta, and J.Jordán (2009).
Superoxide dismutases: a physiopharmacological update.
  J Physiol Biochem, 65, 195-208.  
  19193992 H.L.Pedersen, N.P.Willassen, and I.Leiros (2009).
The first structure of a cold-adapted superoxide dismutase (SOD): biochemical and structural characterization of iron SOD from Aliivibrio salmonicida.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 84-92.
PDB code: 2w7w
19384994 J.F.Bachega, M.V.Navarro, L.Bleicher, R.K.Bortoleto-Bugs, D.Dive, P.Hoffmann, E.Viscogliosi, and R.C.Garratt (2009).
Systematic structural studies of iron superoxide dismutases from human parasites and a statistical coupling analysis of metal binding specificity.
  Proteins, 77, 26-37.
PDB codes: 2goj 2gpc 3esf
19265433 J.J.Perry, A.S.Hearn, D.E.Cabelli, H.S.Nick, J.A.Tainer, and D.N.Silverman (2009).
Contribution of human manganese superoxide dismutase tyrosine 34 to structure and catalysis.
  Biochemistry, 48, 3417-3424.
PDB codes: 1zsp 1zte 1zuq 2p4k
19297238 K.L.Stone, and A.S.Borovik (2009).
Lessons from nature: unraveling biological CH bond activation.
  Curr Opin Chem Biol, 13, 114-118.  
19755112 M.M.Whittaker, and J.W.Whittaker (2009).
In vitro metal uptake by recombinant human manganese superoxide dismutase.
  Arch Biochem Biophys, 491, 69-74.  
18518943 J.M.Kwasigroch, R.Wintjens, D.Gilis, and M.Rooman (2008).
SODa: an Mn/Fe superoxide dismutase prediction and design server.
  BMC Bioinformatics, 9, 257.  
18841998 M.M.Whittaker, and J.W.Whittaker (2008).
Conformationally gated metal uptake by apomanganese superoxide dismutase.
  Biochemistry, 47, 11625-11636.  
18690655 M.Schmidt, S.Zahn, M.Carella, O.Ohlenschläger, M.Görlach, E.Kothe, and J.Weston (2008).
Solution structure of a functional biomimetic and mechanistic implications for nickel superoxide dismutases.
  Chembiochem, 9, 2135-2146.  
17887751 A.Dey, F.E.Jenney, M.W.Adams, M.K.Johnson, K.O.Hodgson, B.Hedman, and E.I.Solomon (2007).
Sulfur K-edge X-ray absorption spectroscopy and density functional theory calculations on superoxide reductase: role of the axial thiolate in reactivity.
  J Am Chem Soc, 129, 12418-12431.  
17522887 Z.Su, M.F.Chai, P.L.Lu, R.An, J.Chen, and X.C.Wang (2007).
AtMTM1, a novel mitochondrial protein, may be involved in activation of the manganese-containing superoxide dismutase in Arabidopsis.
  Planta, 226, 1031-1039.  
16830148 L.Noodleman, and W.G.Han (2006).
Structure, redox, pKa, spin. A golden tetrad for understanding metalloenzyme energetics and reaction pathways.
  J Biol Inorg Chem, 11, 674-694.  
16802319 L.Rulísek, K.P.Jensen, K.Lundgren, and U.Ryde (2006).
The reaction mechanism of iron and manganese superoxide dismutases studied by theoretical calculations.
  J Comput Chem, 27, 1398-1414.  
16258041 M.M.Whittaker, K.Mizuno, H.P.Bächinger, and J.W.Whittaker (2006).
Kinetic analysis of the metal binding mechanism of Escherichia coli manganese superoxide dismutase.
  Biophys J, 90, 598-607.  
  17077482 O.A.Asojo, E.J.Schott, G.R.Vasta, and A.M.Silva (2006).
Structures of PmSOD1 and PmSOD2, two superoxide dismutases from the protozoan parasite Perkinsus marinus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1072-1075.
PDB codes: 2cw2 2cw3
15659371 I.G.Muñoz, J.F.Moran, M.Becana, and G.Montoya (2005).
The crystal structure of an eukaryotic iron superoxide dismutase suggests intersubunit cooperation during catalysis.
  Protein Sci, 14, 387-394.
PDB code: 1unf
15630547 H.A.Haemig, and R.J.Brooker (2004).
Importance of conserved acidic residues in mntH, the Nramp homolog of Escherichia coli.
  J Membr Biol, 201, 97.  
15082717 K.Mizuno, M.M.Whittaker, H.P.Bächinger, and J.W.Whittaker (2004).
Calorimetric studies on the tight binding metal interactions of Escherichia coli manganese superoxide dismutase.
  J Biol Chem, 279, 27339-27344.  
14672935 R.Wintjens, C.Noël, A.C.May, D.Gerbod, F.Dufernez, M.Capron, E.Viscogliosi, and M.Rooman (2004).
Specificity and phenetic relationships of iron- and manganese-containing superoxide dismutases on the basis of structure and sequence comparisons.
  J Biol Chem, 279, 9248-9254.  
12485776 B.Ge, F.W.Scheller, and F.Lisdat (2003).
Electrochemistry of immobilized CuZnSOD and FeSOD and their interaction with superoxide radicals.
  Biosens Bioelectron, 18, 295-302.  
12777777 I.G.Muñoz, J.F.Moran, M.Becana, and G.Montoya (2003).
Crystallization and preliminary X-ray diffraction studies of the eukaryotic iron superoxide dismutase (FeSOD) from Vigna unguiculata.
  Acta Crystallogr D Biol Crystallogr, 59, 1070-1072.  
12730184 L.C.Tabares, C.Bittel, N.Carrillo, A.Bortolotti, and N.Cortez (2003).
The single superoxide dismutase of Rhodobacter capsulatus is a cambialistic, manganese-containing enzyme.
  J Bacteriol, 185, 3223-3227.  
12631270 M.M.Whittaker, V.V.Barynin, T.Igarashi, and J.W.Whittaker (2003).
Outer sphere mutagenesis of Lactobacillus plantarum manganese catalase disrupts the cluster core. Mechanistic implications.
  Eur J Biochem, 270, 1102-1116.
PDB code: 1o9i
12672826 T.Hatta, G.Mukerjee-Dhar, J.Damborsky, H.Kiyohara, and K.Kimbara (2003).
Characterization of a novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from a polychlorinated biphenyl- and naphthalene-degrading Bacillus sp. JF8.
  J Biol Chem, 278, 21483-21492.  
12036008 L.Soulère, C.Viodé, J.Périé, and P.Hoffmann (2002).
Selective inhibition of Fe- versus Cu/Zn-superoxide dismutases by 2,3-dihydroxybenzoic acid derivatives.
  Chem Pharm Bull (Tokyo), 50, 578-582.  
12023089 M.Roux, and J.Covés (2002).
The iron-containing superoxide dismutase of Ralstonia metallidurans CH34.
  FEMS Microbiol Lett, 210, 129-133.  
12392545 T.Hunter, J.V.Bannister, and G.J.Hunter (2002).
Thermostability of manganese- and iron-superoxide dismutases from Escherichia coli is determined by the characteristic position of a glutamine residue.
  Eur J Biochem, 269, 5137-5148.  
12377761 W.B.Greenleaf, and D.N.Silverman (2002).
Activation of the proton transfer pathway in catalysis by iron superoxide dismutase.
  J Biol Chem, 277, 49282-49286.  
11248699 E.De Vendittis, T.Ursby, R.Rullo, M.A.Gogliettino, M.Masullo, and V.Bocchini (2001).
Phenylmethanesulfonyl fluoride inactivates an archaeal superoxide dismutase by chemical modification of a specific tyrosine residue. Cloning, sequencing and expression of the gene coding for Sulfolobus solfataricus superoxide dismutase.
  Eur J Biochem, 268, 1794-1801.  
11443075 G.Silva, J.LeGall, A.V.Xavier, M.Teixeira, and C.Rodrigues-Pousada (2001).
Molecular characterization of Desulfovibrio gigas neelaredoxin, a protein involved in oxygen detoxification in anaerobes.
  J Bacteriol, 183, 4413-4420.  
11114906 H.L.Lumppio, N.V.Shenvi, A.O.Summers, G.Voordouw, and D.M.Kurtz (2001).
Rubrerythrin and rubredoxin oxidoreductase in Desulfovibrio vulgaris: a novel oxidative stress protection system.
  J Bacteriol, 183, 101-108.  
11093266 M.S.Madhusudhan, and S.Vishveshwara (2001).
Computer modeling of human angiogenin-dinucleotide substrate interaction.
  Proteins, 42, 125-135.  
11141052 R.A.Edwards, M.M.Whittaker, J.W.Whittaker, E.N.Baker, and G.B.Jameson (2001).
Outer sphere mutations perturb metal reactivity in manganese superoxide dismutase.
  Biochemistry, 40, 15-27.
PDB codes: 1en4 1en5 1en6
11294629 R.A.Edwards, M.M.Whittaker, J.W.Whittaker, E.N.Baker, and G.B.Jameson (2001).
Removing a hydrogen bond in the dimer interface of Escherichia coli manganese superoxide dismutase alters structure and reactivity.
  Biochemistry, 40, 4622-4632.
PDB codes: 1i08 1i0h
11053832 C.J.Bond, J.Huang, R.Hajduk, K.E.Flick, P.J.Heath, and B.L.Stoddard (2000).
Cloning, sequence and crystallographic structure of recombinant iron superoxide dismutase from Pseudomonas ovalis.
  Acta Crystallogr D Biol Crystallogr, 56, 1359-1366.
PDB code: 1dt0
10848964 S.Sugio, B.Y.Hiraoka, and F.Yamakura (2000).
Crystal structure of cambialistic superoxide dismutase from porphyromonas gingivalis.
  Eur J Biochem, 267, 3487-3495.
PDB code: 1qnn
10852710 V.J.Lévêque, M.E.Stroupe, J.R.Lepock, D.E.Cabelli, J.A.Tainer, H.S.Nick, and D.N.Silverman (2000).
Multiple replacements of glutamine 143 in human manganese superoxide dismutase: effects on structure, stability, and catalysis.
  Biochemistry, 39, 7131-7137.
PDB code: 1em1
10455106 A.S.Hearn, C.Tu, H.S.Nick, and D.N.Silverman (1999).
Characterization of the product-inhibited complex in catalysis by human manganese superoxide dismutase.
  J Biol Chem, 274, 24457-24460.  
10488113 C.A.Ramilo, V.Leveque, Y.Guan, J.R.Lepock, J.A.Tainer, H.S.Nick, and D.N.Silverman (1999).
Interrupting the hydrogen bond network at the active site of human manganese superoxide dismutase.
  J Biol Chem, 274, 27711-27716.
PDB code: 2gds
10585544 C.B.Baert, P.Deloron, E.Viscogliosi, M.Dauchez, D.Camus, and D.Dive (1999).
Analysis of genetic diversity at the iron-containing superoxide dismutase locus in Plasmodium falciparum wild isolates.
  FEMS Microbiol Lett, 181, 237-243.  
10574944 M.M.Whittaker, and J.W.Whittaker (1999).
Thermally triggered metal binding by recombinant Thermus thermophilus manganese superoxide dismutase, expressed as the apo-enzyme.
  J Biol Chem, 274, 34751-34757.  
10231372 M.Schmidt (1999).
Manipulating the coordination mumber of the ferric iron within the cambialistic superoxide dismutase of Propionibacterium shermanii by changing the pH-value A crystallographic analysis.
  Eur J Biochem, 262, 117-127.
PDB codes: 1bs3 1bsm 1bt8
  10419947 R.Santos, S.Bocquet, A.Puppo, and D.Touati (1999).
Characterization of an atypical superoxide dismutase from Sinorhizobium meliloti.
  J Bacteriol, 181, 4509-4516.  
10090763 S.B.Choudhury, J.W.Lee, G.Davidson, Y.I.Yim, K.Bose, M.L.Sharma, S.O.Kang, D.E.Cabelli, and M.J.Maroney (1999).
Examination of the nickel site structure and reaction mechanism in Streptomyces seoulensis superoxide dismutase.
  Biochemistry, 38, 3744-3752.  
9548935 C.K.Vance, and A.F.Miller (1998).
Spectroscopic comparisons of the pH dependencies of Fe-substituted (Mn)superoxide dismutase and Fe-superoxide dismutase.
  Biochemistry, 37, 5518-5527.  
9698380 C.L.Borders, M.J.Bjerrum, M.A.Schirmer, and S.G.Oliver (1998).
Characterization of recombinant Saccharomyces cerevisiae manganese-containing superoxide dismutase and its H30A and K170R mutants expressed in Escherichia coli.
  Biochemistry, 37, 11323-11331.  
9922163 C.Pham, J.Jankun, E.Skrzypczak-Jankun, R.A.Flowers, and M.O.Funk (1998).
Structural and thermochemical characterization of lipoxygenase-catechol complexes.
  Biochemistry, 37, 17952-17957.
PDB code: 1byt
9582345 C.Su, and E.H.Oliw (1998).
Manganese lipoxygenase. Purification and characterization.
  J Biol Chem, 273, 13072-13079.  
9603906 F.Yamakura, H.Taka, T.Fujimura, and K.Murayama (1998).
Inactivation of human manganese-superoxide dismutase by peroxynitrite is caused by exclusive nitration of tyrosine 34 to 3-nitrotyrosine.
  J Biol Chem, 273, 14085-14089.  
9485360 R.W.Frazee, A.M.Orville, K.B.Dolbeare, H.Yu, D.H.Ohlendorf, and J.D.Lipscomb (1998).
The axial tyrosinate Fe3+ ligand in protocatechuate 3,4-dioxygenase influences substrate binding and product release: evidence for new reaction cycle intermediates.
  Biochemistry, 37, 2131-2144.
PDB code: 3pcd
9537987 Y.Guan, M.J.Hickey, G.E.Borgstahl, R.A.Hallewell, J.R.Lepock, D.O'Connor, Y.Hsieh, H.S.Nick, D.N.Silverman, and J.A.Tainer (1998).
Crystal structure of Y34F mutant human mitochondrial manganese superoxide dismutase and the functional role of tyrosine 34.
  Biochemistry, 37, 4722-4730.
PDB codes: 1ap5 1ap6
9537988 Y.Hsieh, Y.Guan, C.Tu, P.J.Bratt, A.Angerhofer, J.R.Lepock, M.J.Hickey, J.A.Tainer, H.S.Nick, and D.N.Silverman (1998).
Probing the active site of human manganese superoxide dismutase: the role of glutamine 143.
  Biochemistry, 37, 4731-4739.
PDB code: 1qnm
9428655 A.Dello Russo, R.Rullo, G.Nitti, M.Masullo, and V.Bocchini (1997).
Iron superoxide dismutase from the archaeon Sulfolobus solfataricus: average hydrophobicity and amino acid weight are involved in the adaptation of proteins to extreme environments.
  Biochim Biophys Acta, 1343, 23-30.  
9254600 A.M.Orville, J.D.Lipscomb, and D.H.Ohlendorf (1997).
Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: endogenous Fe3+ ligand displacement in response to substrate binding.
  Biochemistry, 36, 10052-10066.
PDB codes: 3pca 3pcj 3pck 3pcl 3pcm
9125513 D.L.Sorkin, and A.F.Miller (1997).
Spectroscopic measurement of a long-predicted active site pK in iron-superoxide dismutase from Escherichia coli.
  Biochemistry, 36, 4916-4924.  
9204864 D.L.Sorkin, D.K.Duong, and A.F.Miller (1997).
Mutation of tyrosine 34 to phenylalanine eliminates the active site pK of reduced iron-containing superoxide dismutase.
  Biochemistry, 36, 8202-8208.  
9461283 E.L.Hegg, and L.Que (1997).
The 2-His-1-carboxylate facial triad--an emerging structural motif in mononuclear non-heme iron(II) enzymes.
  Eur J Biochem, 250, 625-629.  
9220980 M.M.Whittaker, and J.W.Whittaker (1997).
Mutagenesis of a proton linkage pathway in Escherichia coli manganese superoxide dismutase.
  Biochemistry, 36, 8923-8931.  
9125514 T.Hunter, K.Ikebukuro, W.H.Bannister, J.V.Bannister, and G.J.Hunter (1997).
The conserved residue tyrosine 34 is essential for maximal activity of iron-superoxide dismutase from Escherichia coli.
  Biochemistry, 36, 4925-4933.  
9047314 Y.R.Boldt, A.K.Whiting, M.L.Wagner, M.J.Sadowsky, L.Que, and L.P.Wackett (1997).
Manganese(II) active site mutants of 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Arthrobacter globiformis strain CM-2.
  Biochemistry, 36, 2147-2153.  
8555170 A.K.Whiting, Y.R.Boldt, M.P.Hendrich, L.P.Wackett, and L.Que (1996).
Manganese(II)-dependent extradiol-cleaving catechol dioxygenase from Arthrobacter globiformis CM-2.
  Biochemistry, 35, 160-170.  
8663465 J.L.Hsu, Y.Hsieh, C.Tu, D.O'Connor, H.S.Nick, and D.N.Silverman (1996).
Catalytic properties of human manganese superoxide dismutase.
  J Biol Chem, 271, 17687-17691.  
8639627 M.M.Whittaker, and J.W.Whittaker (1996).
Low-temperature thermochromism marks a change in coordination for the metal ion in manganese superoxide dismutase.
  Biochemistry, 35, 6762-6770.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.