PDBsum entry 1en5

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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
Protein chains
205 a.a. *
_MN ×4
Waters ×309
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure analysis of the e. Coli manganese superoxide dismutase y34f mutant
Structure: Manganese superoxide dismutase. Chain: a, b, c, d. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
2.30Å     R-factor:   0.167     R-free:   0.195
Authors: R.A.Edwards,M.M.Whittaker,E.N.Baker,J.W.Whittaker, G.B.Jameson
Key ref:
R.A.Edwards et al. (2001). Outer sphere mutations perturb metal reactivity in manganese superoxide dismutase. Biochemistry, 40, 15-27. PubMed id: 11141052 DOI: 10.1021/bi0018943
20-Mar-00     Release date:   27-Jun-01    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P00448  (SODM_ECOLI) -  Superoxide dismutase [Mn]
206 a.a.
205 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Superoxide dismutase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 superoxide + 2 H+ = O2 + H2O2
2 × superoxide
+ 2 × H(+)
= O(2)
+ H(2)O(2)
      Cofactor: Fe cation or Mn(2+) or (Zn(2+) and Cu cation)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     cellular response to selenium ion   7 terms 
  Biochemical function     antioxidant activity     6 terms  


    Added reference    
DOI no: 10.1021/bi0018943 Biochemistry 40:15-27 (2001)
PubMed id: 11141052  
Outer sphere mutations perturb metal reactivity in manganese superoxide dismutase.
R.A.Edwards, M.M.Whittaker, J.W.Whittaker, E.N.Baker, G.B.Jameson.
Tyrosine 34 and glutamine 146 are highly conserved outer sphere residues in the mononuclear manganese active site of Escherichia coli manganese superoxide dismutase. Biochemical and spectroscopic characterization of site-directed mutants has allowed functional characterization of these residues in the wild-type (wt) enzyme. X-ray crystallographic analysis of three mutants (Y34F, Q146L, and Q146H) reveal subtle changes in the protein structures. The Y34A mutant, as well as the previously reported Y34F mutant, retained essentially the full superoxide dismutase activity of the wild-type enzyme, and the X-ray crystal structure of Y34F manganese superoxide dismutase shows that mutation of this strictly conserved residue has only minor effects on the positions of active site residues and the organized water in the substrate access funnel. Mutation of the outer sphere solvent pocket residue Q146 has more dramatic effects. The Q146E mutant is isolated as an apoprotein lacking dismutase activity. Q146L and Q146H mutants retain only 5-10% of the dismutase activity of the wild-type enzyme. The absorption and circular dichroism spectra of the Q146H mutant resemble corresponding data for the superoxide dismutase from a hyperthermophilic archaeon, Pyrobaculum aerophilum, which is active in both Mn and Fe forms. Interestingly, the iron-substituted Q146H protein also exhibits low dismutase activity, which increases at lower pH. Mutation of glutamine 146 disrupts the hydrogen-bonding network in the active site and has a greater effect on protein structure than does the Y34F mutant, with rearrangement of the tyrosine 34 and tryptophan 128 side chains.

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
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
18685763 L.Cuesta, E.Tomat, V.M.Lynch, and J.L.Sessler (2008).
Binuclear organometallic ruthenium complexes of a Schiff base expanded porphyrin.
  Chem Commun (Camb), (), 3744-3746.  
18841998 M.M.Whittaker, and J.W.Whittaker (2008).
Conformationally gated metal uptake by apomanganese superoxide dismutase.
  Biochemistry, 47, 11625-11636.  
17459326 D.Svedruzi─ç, Y.Liu, L.A.Reinhardt, E.Wroclawska, W.W.Cleland, and N.G.Richards (2007).
Investigating the roles of putative active site residues in the oxalate decarboxylase from Bacillus subtilis.
  Arch Biochem Biophys, 464, 36-47.  
15583971 A.Yilmaz, R.A.Sari, M.Gundogdu, N.Kose, and E.Dag (2005).
Trace elements and some extracellular antioxidant proteins levels in serum of patients with systemic lupus erythematosus.
  Clin Rheumatol, 24, 331-335.  
15999386 E.Sartori, C.Corvaja, S.Oancea, F.Formaggio, M.Crisma, and C.Toniolo (2005).
Linear configuration of the spins of a stable trinitroxide radical based on a ternary helical peptide.
  Chemphyschem, 6, 1472-1475.  
15750996 H.Hong, J.B.Spencer, J.L.Porter, P.F.Leadlay, and T.Stinear (2005).
A novel mycolactone from a clinical isolate of Mycobacterium ulcerans provides evidence for additional toxin heterogeneity as a result of specific changes in the modular polyketide synthase.
  Chembiochem, 6, 643-648.  
  16511113 I.W.Boucher, A.K.Kalliomaa, V.M.Levdikov, E.V.Blagova, M.J.Fogg, J.A.Brannigan, K.S.Wilson, and A.J.Wilkinson (2005).
Structures of two superoxide dismutases from Bacillus anthracis reveal a novel active centre.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 621-624.
PDB codes: 1xre 1xuq
15062777 A.F.Miller (2004).
Superoxide dismutases: active sites that save, but a protein that kills.
  Curr Opin Chem Biol, 8, 162-168.  
15173586 J.Wuerges, J.W.Lee, Y.I.Yim, H.S.Yim, S.O.Kang, and K.Djinovic Carugo (2004).
Crystal structure of nickel-containing superoxide dismutase reveals another type of active site.
  Proc Natl Acad Sci U S A, 101, 8569-8574.
PDB codes: 1q0d 1q0f 1q0g 1q0k 1q0m
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.  
15472987 W.Zhong, D.Alexeev, I.Harvey, M.Guo, D.J.Hunter, H.Zhu, D.J.Campopiano, and P.J.Sadler (2004).
Assembly of an oxo-zirconium(IV) cluster in a protein cleft.
  Angew Chem Int Ed Engl, 43, 5914-5918.
PDB code: 1xc1
12481333 A.Specht, P.Bernard, M.Goeldner, and L.Peng (2002).
Mutually induced formation of host-guest complexes between p-sulfonated calix[8]arene and photolabile cholinergic ligands.
  Angew Chem Int Ed Engl, 41, 4706-4708.  
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.  
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
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.