PDBsum entry 1xdc

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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
Jmol PyMol
Protein chains
198 a.a. *
_MN ×2
Waters ×449
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Hydrogen bonding in human manganese superoxide dismutase con fluorotyrosine
Structure: Superoxide dismutase [mn], mitochondrial. Chain: a, b. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: sod2. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
1.85Å     R-factor:   0.212     R-free:   0.252
Authors: I.Ayala,J.J.Perry,J.Szczepanski,D.E.Cabelli,J.A.Tainer,M.T.V H.S.Nick,D.N.Silverman
Key ref: I.Ayala et al. (2005). Hydrogen bonding in human manganese superoxide dismutase containing 3-fluorotyrosine. Biophys J, 89, 4171-4179. PubMed id: 16150974
05-Sep-04     Release date:   22-Mar-05    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P04179  (SODM_HUMAN) -  Superoxide dismutase [Mn], mitochondrial
222 a.a.
198 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 9 residue positions (black crosses)

 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!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     superoxide dismutase activity     2 terms  


    Added reference    
Biophys J 89:4171-4179 (2005)
PubMed id: 16150974  
Hydrogen bonding in human manganese superoxide dismutase containing 3-fluorotyrosine.
I.Ayala, J.J.Perry, J.Szczepanski, J.A.Tainer, M.T.Vala, H.S.Nick, D.N.Silverman.
Incorporation of 3-fluorotyrosine and site-specific mutagenesis has been utilized with Fourier transform infrared (FTIR) spectroscopy and x-ray crystallography to elucidate active-site structure and the role of an active-site residue Tyr34 in human manganese superoxide dismutase (MnSOD). Calculated harmonic frequencies at the B3LYP/6-31G** level of theory for L-tyrosine and its 3-fluorine substituted analog are compared to experimental frequencies for vibrational mode assignments. Each of the nine tyrosine residues in each of the four subunits of the homotetramer of human MnSOD was replaced with 3-fluorotyrosine. The crystal structures of the unfluorinated and fluorinated wild-type MnSOD are nearly superimposable with the root mean-square deviation for 198 alpha-carbon atoms at 0.3 A. The FTIR data show distinct vibrational modes arising from 3-fluorotyrosine in MnSOD. Comparison of spectra for wild-type and Y34F MnSOD showed that the phenolic hydroxyl of Tyr34 is hydrogen bonded, acting as a proton donor in the active site. Comparison with crystal structures demonstrates that the hydroxyl of Tyr34 is a hydrogen bond donor to an adjacent water molecule; this confirms the participation of Tyr34 in a network of residues and water molecules that extends from the active site to the adjacent subunit.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19265377 F.Rappaport, A.Boussac, D.A.Force, J.Peloquin, M.Brynda, M.Sugiura, S.Un, R.D.Britt, and B.A.Diner (2009).
Probing the coupling between proton and electron transfer in photosystem II core complexes containing a 3-fluorotyrosine.
  J Am Chem Soc, 131, 4425-4433.  
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
17915350 G.Cornilescu, E.B.Hadley, M.G.Woll, J.L.Markley, S.H.Gellman, and C.C.Cornilescu (2007).
Solution structure of a small protein containing a fluorinated side chain in the core.
  Protein Sci, 16, 2089.  
17174478 J.J.Perry, L.Fan, and J.A.Tainer (2007).
Developing master keys to brain pathology, cancer and aging from the structural biology of proteins controlling reactive oxygen species and DNA repair.
  Neuroscience, 145, 1280-1299.  
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