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PDBsum entry 2p4k

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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
2p4k
Jmol
Contents
Protein chains
198 a.a. *
Metals
_MN ×4
Waters ×1202
* Residue conservation analysis
PDB id:
2p4k
Name: Oxidoreductase
Title: Contribution to structure and catalysis of tyrosine 34 in human manganese superoxide dismutase
Structure: Superoxide dismutase. Chain: a, b, c, d. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: sod2. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.48Å     R-factor:   0.160     R-free:   0.222
Authors: J.J.Perry
Key ref: J.J.Perry et al. (2009). Contribution of human manganese superoxide dismutase tyrosine 34 to structure and catalysis. Biochemistry, 48, 3417-3424. PubMed id: 19265433
Date:
12-Mar-07     Release date:   03-Apr-07    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04179  (SODM_HUMAN) -  Superoxide dismutase [Mn], mitochondrial
Seq:
Struc:
222 a.a.
198 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.1.15.1.1  - 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!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     superoxide dismutase activity     2 terms  

 

 
    Added reference    
 
 
Biochemistry 48:3417-3424 (2009)
PubMed id: 19265433  
 
 
Contribution of human manganese superoxide dismutase tyrosine 34 to structure and catalysis.
J.J.Perry, A.S.Hearn, D.E.Cabelli, H.S.Nick, J.A.Tainer, D.N.Silverman.
 
  ABSTRACT  
 
Superoxide dismutase (SOD) enzymes are critical in controlling levels of reactive oxygen species (ROS) that are linked to aging, cancer, and neurodegenerative disease. Superoxide (O(2)(*-)) produced during respiration is removed by the product of the SOD2 gene, the homotetrameric manganese superoxide dismutase (MnSOD). Here, we examine the structural and catalytic roles of the highly conserved active-site residue Tyr34, based upon structure-function studies of MnSOD enzymes with mutations at this site. Substitution of Tyr34 with five different amino acids retained the active-site protein structure and assembly but caused a substantial decrease in the catalytic rate constant for the reduction of superoxide. The rate constant for formation of the product inhibition complex also decreases but to a much lesser extent, resulting in a net increase in the level of product inhibited form of the mutant enzymes. Comparisons of crystal structures and catalytic rates also suggest that one mutation, Y34V, interrupts the hydrogen-bonded network, which is associated with a rapid dissociation of the product-inhibited complex. Notably, with three of the Tyr34 mutants, we also observe an intermediate in catalysis, which has not been reported previously. Thus, these mutants establish a means of trapping a catalytic intermediate that promises to help elucidate the mechanism of catalysis.
 

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
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.