PDBsum entry 2adp

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protein metals links
Oxidoreductase PDB id
Protein chain
196 a.a. *
Waters ×46
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Nitrated human manganese superoxide dismutase
Structure: Superoxide dismutase [mn]. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: sod2. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PDB file)
2.40Å     R-factor:   0.197     R-free:   0.218
Authors: P.Quint,R.Reutzel,R.Mikulski,R.Mckenna,D.N.Silverman
Key ref: P.Quint et al. (2006). Crystal structure of nitrated human manganese superoxide dismutase: mechanism of inactivation. Free Radic Biol Med, 40, 453-458. PubMed id: 16443160 DOI: 10.1016/j.freeradbiomed.2005.08.045
20-Jul-05     Release date:   04-Jul-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P04179  (SODM_HUMAN) -  Superoxide dismutase [Mn], mitochondrial
222 a.a.
196 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!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     superoxide dismutase activity     2 terms  


    Added reference    
DOI no: 10.1016/j.freeradbiomed.2005.08.045 Free Radic Biol Med 40:453-458 (2006)
PubMed id: 16443160  
Crystal structure of nitrated human manganese superoxide dismutase: mechanism of inactivation.
P.Quint, R.Reutzel, R.Mikulski, R.McKenna, D.N.Silverman.
A cellular consequence of the reaction of superoxide and nitric oxide is enhanced peroxynitrite levels. Reaction of peroxynitrite with manganese superoxide dismutase (MnSOD) causes nitration of the active-site residue Tyr34 and nearly complete inhibition of catalysis. We report the crystal structures at 2.4 A resolution of human MnSOD nitrated by peroxynitrite and the unmodified MnSOD. A comparison of these structures showed no significant conformational changes of active-site residues or solvent displacement. The side chain of 3-nitrotyrosine 34 had a single conformation that extended toward the manganese with O1 of the nitro group within hydrogen-bonding distance (3.1 A) of Nepsilon2 of the second-shell ligand Gln143. Also, nitration of Tyr34 caused a weakening, as evidenced by the lengthening, of a hydrogen bond between its phenolic OH and Gln143, part of an extensive hydrogen-bond network in the active site. Inhibition of catalysis can be attributed to a steric effect of 3-nitrotyrosine 34 that impedes substrate access and binding, and alteration of the hydrogen-bond network that supports proton transfer in catalysis. It is also possible that an electrostatic effect of the nitro group has altered the finely tuned redox potential necessary for efficient catalysis, although the redox potential of nitrated MnSOD has not been measured.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21264418 M.E.Moral, C.Tu, W.Imaram, A.Angerhofer, D.N.Silverman, and N.G.Richards (2011).
Nitric oxide reversibly inhibits Bacillus subtilis oxalate decarboxylase.
  Chem Commun (Camb), 47, 3111-3113.  
19662443 G.Y.Park, S.Deepalatha, S.C.Puiu, D.H.Lee, B.Mondal, A.A.Narducci Sarjeant, D.del Rio, M.Y.Pau, E.I.Solomon, and K.D.Karlin (2009).
A peroxynitrite complex of copper: formation from a copper-nitrosyl complex, transformation to nitrite and exogenous phenol oxidative coupling or nitration.
  J Biol Inorg Chem, 14, 1301-1311.  
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
19297238 K.L.Stone, and A.S.Borovik (2009).
Lessons from nature: unraveling biological CH bond activation.
  Curr Opin Chem Biol, 13, 114-118.  
19539749 M.A.Abdelmegeed, K.H.Moon, J.P.Hardwick, F.J.Gonzalez, and B.J.Song (2009).
Role of peroxisome proliferator-activated receptor-alpha in fasting-mediated oxidative stress.
  Free Radic Biol Med, 47, 767-778.  
19284298 M.Safinowski, B.Wilhelm, T.Reimer, A.Weise, N.Thomé, H.Hänel, T.Forst, and A.Pfützner (2009).
Determination of nitrotyrosine concentrations in plasma samples of diabetes mellitus patients by four different immunoassays leads to contradictive results and disqualifies the majority of the tests.
  Clin Chem Lab Med, 47, 483-488.  
  18084079 P.Liu, H.E.Ewis, Y.J.Huang, C.D.Lu, P.C.Tai, and I.T.Weber (2007).
Structure of Bacillus subtilis superoxide dismutase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 1003-1007.
PDB code: 2rcv
17077966 S.Bartesaghi, G.Ferrer-Sueta, G.Peluffo, V.Valez, H.Zhang, B.Kalyanaraman, and R.Radi (2007).
Protein tyrosine nitration in hydrophilic and hydrophobic environments.
  Amino Acids, 32, 501-515.  
17603493 S.Nagaraj, K.Gupta, V.Pisarev, L.Kinarsky, S.Sherman, L.Kang, D.L.Herber, J.Schneck, and D.I.Gabrilovich (2007).
Altered recognition of antigen is a mechanism of CD8+ T cell tolerance in cancer.
  Nat Med, 13, 828-835.  
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.