PDBsum entry 3g4x

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Oxidoreductase PDB id
Protein chains
117 a.a. *
_CL ×3
_NI ×3
Waters ×389
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure of nisod y9f mutant
Structure: Superoxide dismutase [ni]. Chain: a, b, c. Fragment: nisod (unp residues 15 to 131). Synonym: nisod, nickel-containing superoxide dismutase. Engineered: yes. Mutation: yes
Source: Streptomyces coelicolor. Organism_taxid: 1902. Gene: 2sc7g11.16c, sco5254, sod1, sodn. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.01Å     R-factor:   0.172     R-free:   0.237
Authors: S.C.Garman,A.I.Guce,R.W.Herbst,P.A.Bryngelson,D.E.Cabelli, K.A.Higgins,K.C.Ryan,M.J.Maroney
Key ref: R.W.Herbst et al. (2009). Role of conserved tyrosine residues in NiSOD catalysis: a case of convergent evolution. Biochemistry, 48, 3354-3369. PubMed id: 19183068 DOI: 10.1021/bi802029t
04-Feb-09     Release date:   28-Apr-09    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P80735  (SODN_STRCO) -  Superoxide dismutase [Ni]
131 a.a.
117 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: 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!
  Biochemical function     antioxidant activity     3 terms  


    Added reference    
DOI no: 10.1021/bi802029t Biochemistry 48:3354-3369 (2009)
PubMed id: 19183068  
Role of conserved tyrosine residues in NiSOD catalysis: a case of convergent evolution.
R.W.Herbst, A.Guce, P.A.Bryngelson, K.A.Higgins, K.C.Ryan, D.E.Cabelli, S.C.Garman, M.J.Maroney.
Superoxide dismutases rely on protein structural elements to adjust the redox potential of the metallocenter to an optimum value near 300 mV (vs NHE), to provide a source of protons for catalysis, and to control the access of anions to the active site. These aspects of the catalytic mechanism are examined herein for recombinant preparations of the nickel-dependent SOD (NiSOD) from Streptomyces coelicolor and for a series of mutants that affect a key tyrosine residue, Tyr9 (Y9F-, Y62F-, Y9F/Y62F-, and D3A-NiSOD). Structural aspects of the nickel sites are examined by a combination of EPR and X-ray absorption spectroscopies, and by single-crystal X-ray diffraction at approximately 1.9 A resolution in the case of Y9F- and D3A-NiSODs. The functional effects of the mutations are examined by kinetic studies employing pulse radiolytic generation of O2- and by redox titrations. These studies reveal that although the structure of the nickel center in NiSOD is unique, the ligand environment is designed to optimize the redox potential at 290 mV and results in the oxidation of 50% of the nickel centers in the oxidized hexamer. Kinetic investigations show that all of the mutant proteins have considerable activity. In the case of Y9F-NiSOD, the enzyme exhibits saturation behavior that is not observed in wild-type (WT) NiSOD and suggests that release of peroxide is inhibited. The crystal structure of Y9F-NiSOD reveals an anion binding site that is occupied by either Cl- or Br- and is located close to but not within bonding distance of the nickel center. The structure of D3A-NiSOD reveals that in addition to affecting the interaction between subunits, this mutation repositions Tyr9 and leads to altered chemistry with peroxide. Comparisons with Mn(SOD) and Fe(SOD) reveal that although different strategies for adjusting the redox potential and supply of protons are employed, NiSOD has evolved a similar strategy for controlling the access of anions to the active site.

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
20000358 M.E.Krause, A.M.Glass, T.A.Jackson, and J.S.Laurence (2010).
Novel tripeptide model of nickel superoxide dismutase.
  Inorg Chem, 49, 362-364.  
20333422 O.E.Johnson, K.C.Ryan, M.J.Maroney, and T.C.Brunold (2010).
Spectroscopic and computational investigation of three Cys-to-Ser mutants of nickel superoxide dismutase: insight into the roles played by the Cys2 and Cys6 active-site residues.
  J Biol Inorg Chem, 15, 777-793.  
19894770 J.Shearer, K.P.Neupane, and P.E.Callan (2009).
Metallopeptide based mimics with substituted histidines approximate a key hydrogen bonding network in the metalloenzyme nickel superoxide dismutase.
  Inorg Chem, 48, 10560-10571.  
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