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Oxidoreductase PDB id
Protein chains
191 a.a. *
_FE ×4
Waters ×504
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure of porphyromonas gingivalis sod
Structure: Superoxide dismutase. Chain: a, b, c, d. Synonym: sod. Engineered: yes
Source: Porphyromonas gingivalis. Organism_taxid: 837. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
1.60Å     R-factor:   0.231     R-free:   0.256
Authors: F.Yamakura,S.Sugio,B.Y.Hiraoka,T.Yokota,D.Ohmori
Key ref:
F.Yamakura et al. (2003). Pronounced conversion of the metal-specific activity of superoxide dismutase from Porphyromonas gingivalis by the mutation of a single amino acid (Gly155Thr) located apart from the active site. Biochemistry, 42, 10790-10799. PubMed id: 12962504 DOI: 10.1021/bi0349625
20-May-03     Release date:   20-May-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P19665  (SODF_PORGI) -  Superoxide dismutase [Mn/Fe]
191 a.a.
191 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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: Iron or manganese or (zinc and copper)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     oxidoreductase activity     3 terms  


    Added reference    
DOI no: 10.1021/bi0349625 Biochemistry 42:10790-10799 (2003)
PubMed id: 12962504  
Pronounced conversion of the metal-specific activity of superoxide dismutase from Porphyromonas gingivalis by the mutation of a single amino acid (Gly155Thr) located apart from the active site.
F.Yamakura, S.Sugio, B.Y.Hiraoka, D.Ohmori, T.Yokota.
Glycine 155, which is located approximately 10 A from the active metal sites, is mostly conserved in aligned amino acid sequences of manganese-specific superoxide dismutases (Mn-SODs) and cambialistic SOD (showing the same activity with Fe and Mn) from Porphyromonas gingivalis, but is substituted for threonine in most Fe-SODs. Since Thr155 is located between Trp123 and Trp125, and Trp123 is one member of the metal-surrounding aromatic amino acids, there is a possibility that the conversion of this amino acid may cause a conversion of the metal-specific activity of cambialistic P. gingivalis SOD. To clarify this possibility, we have prepared a mutant of the P. gingivalis SOD with conversion of Gly155 to Thr. The ratios of the specific activities of Fe- to Mn-reconstituted enzyme, which are measured by the xanthine oxidase/cytochrome c method, increased from 0.6 in the wild-type to 11.2 in the mutant SODs, indicating the conversion of the metal-specific activity of the enzyme from a cambialistic type to an Fe-specific type. The visible absorption spectra of the Fe- and Mn-reconstituted mutant SODs closely resembled those of Fe-specific SOD. Furthermore, the EPR spectra of the Fe- and Mn-reconstituted mutant SODs also closely resembled those of Fe-specific SOD. Three-dimensional structures of the Fe-reconstituted wild-type SOD and Mn-reconstituted mutant SOD have been determined at 1.6 A resolution. Both structures have identical conformations, orientations of residues involved in metal binding, and hydrogen bond networks, while the side chain of Trp123 is moved further toward the metal-binding site than in wild-type SOD. A possible contribution of the structural differences to the conversion of the metal-specific activity through rearrangement of the hydrogen bond network among Trp123, Gln70, Tyr35, and the metal-coordinated solvent is discussed.

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
19191037 T.Wang, A.Qiu, F.Meng, and H.Zhou (2009).
Changing the Metal Binding Specificity of Superoxide Dismutase from Thermus thermophilus HB-27 by a Single Mutation.
  Mol Biotechnol, 42, 146-153.  
17912757 R.Wintjens, D.Gilis, and M.Rooman (2008).
Mn/Fe superoxide dismutase interaction fingerprints and prediction of oligomerization and metal cofactor from sequence.
  Proteins, 70, 1564-1577.  
15062777 A.F.Miller (2004).
Superoxide dismutases: active sites that save, but a protein that kills.
  Curr Opin Chem Biol, 8, 162-168.  
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.  
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