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PDBsum entry 1yai

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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
1yai
Jmol
Contents
Protein chains
151 a.a. *
Metals
_ZN ×3
_CU ×3
Waters ×358
* Residue conservation analysis
PDB id:
1yai
Name: Oxidoreductase
Title: X-ray structure of a bacterial copper,zinc superoxide dismutase
Structure: Copper, zinc superoxide dismutase. Chain: a, b, c. Synonym: cu, zn superoxide dismutase, cu, zn sod. Engineered: yes
Source: Photobacterium leiognathi. Organism_taxid: 658. Strain: mc1061. Gene: phsod. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
1.90Å     R-factor:   0.149     R-free:   0.210
Authors: Y.Bourne,S.M.Redford,T.P.Lo,J.A.Tainer,E.D.Getzoff
Key ref: Y.Bourne et al. (1996). Novel dimeric interface and electrostatic recognition in bacterial Cu,Zn superoxide dismutase. Proc Natl Acad Sci U S A, 93, 12774-12779. PubMed id: 8917495
Date:
03-Feb-96     Release date:   20-Aug-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00446  (SODC_PHOLE) -  Superoxide dismutase [Cu-Zn]
Seq:
Struc:
173 a.a.
151 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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!
  Cellular component     periplasmic space   1 term 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     antioxidant activity     4 terms  

 

 
    Added reference    
 
 
Proc Natl Acad Sci U S A 93:12774-12779 (1996)
PubMed id: 8917495  
 
 
Novel dimeric interface and electrostatic recognition in bacterial Cu,Zn superoxide dismutase.
Y.Bourne, S.M.Redford, H.M.Steinman, J.R.Lepock, J.A.Tainer, E.D.Getzoff.
 
  ABSTRACT  
 
Eukaryotic Cu,Zn superoxide dismutases (CuZnSODs) are antioxidant enzymes remarkable for their unusually stable beta-barrel fold and dimer assembly, diffusion-limited catalysis, and electrostatic guidance of their free radical substrate. Point mutations of CuZnSOD cause the fatal human neurodegenerative disease amyotrophic lateral sclerosis. We determined and analyzed the first crystallographic structure (to our knowledge) for CuZnSOD from a prokaryote, Photobacterium leiognathi, a luminescent symbiont of Leiognathid fish. This structure, exemplifying prokaryotic CuZnSODs, shares the active-site ligand geometry and the topology of the Greek key beta-barrel common to the eukaryotic CuZnSODs. However, the beta-barrel elements recruited to form the dimer interface, the strategy used to forge the channel for electrostatic recognition of superoxide radical, and the connectivity of the intrasubunit disulfide bond in P. leiognathi CuZnSOD are discrete and strikingly dissimilar from those highly conserved in eukaryotic CuZnSODs. This new CuZnSOD structure broadens our understanding of structural features necessary and sufficient for CuZnSOD activity, highlights a hitherto unrecognized adaptability of the Greek key beta-barrel building block in evolution, and reveals that prokaryotic and eukaryotic enzymes diverged from one primordial CuZnSOD and then converged to distinct dimeric enzymes with electrostatic substrate guidance.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19063897 D.S.Shin, M.Didonato, D.P.Barondeau, G.L.Hura, C.Hitomi, J.A.Berglund, E.D.Getzoff, S.C.Cary, and J.A.Tainer (2009).
Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis.
  J Mol Biol, 385, 1534-1555.
PDB codes: 3f7k 3f7l
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
18828904 M.D'Orazio, R.Scotti, L.Nicolini, L.Cervoni, G.Rotilio, A.Battistoni, and R.Gabbianelli (2008).
Regulatory and structural properties differentiating the chromosomal and the bacteriophage-associated Escherichia coli O157:H7 Cu, Zn superoxide dismutases.
  BMC Microbiol, 8, 166.  
18078545 C.D.Putnam, M.Hammel, G.L.Hura, and J.A.Tainer (2007).
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.
  Q Rev Biophys, 40, 191-285.  
16460273 M.P.Lesser (2006).
Oxidative stress in marine environments: biochemistry and physiological ecology.
  Annu Rev Physiol, 68, 253-278.  
15681652 L.Maragliano, M.Falconi, A.Sergi, P.Cioni, S.Castelli, A.Lania, M.E.Stroppolo, G.Strambini, M.Ferrario, and A.Desideri (2005).
Experimental and simulative dissociation of dimeric Cu,Zn superoxide dismutase doubly mutated at the intersubunit surface.
  Biophys J, 88, 2875-2882.  
15135531 D.H.Kho, S.B.Yoo, J.S.Kim, E.J.Kim, and J.K.Lee (2004).
Characterization of Cu- and Zn-containing superoxide dismutase of Rhodobacter sphaeroides.
  FEMS Microbiol Lett, 234, 261-267.  
15449711 R.Gabbianelli, M.D'Orazio, F.Pacello, P.O'Neill, L.Nicolini, G.Rotilio, and A.Battistoni (2004).
Distinctive functional features in prokaryotic and eukaryotic Cu,Zn superoxide dismutases.
  Biol Chem, 385, 749-754.  
15333927 R.M.Cardoso, C.H.Silva, A.P.Ulian de Araújo, T.Tanaka, M.Tanaka, and R.C.Garratt (2004).
Structure of the cytosolic Cu,Zn superoxide dismutase from Schistosoma mansoni.
  Acta Crystallogr D Biol Crystallogr, 60, 1569-1578.
PDB codes: 1to4 1to5
12784219 M.Falconi, M.Brunelli, A.Pesce, M.Ferrario, M.Bolognesi, and A.Desideri (2003).
Static and dynamic water molecules in Cu,Zn superoxide dismutase.
  Proteins, 51, 607-615.  
12944259 R.R.Gabdoulline, U.Kummer, L.F.Olsen, and R.C.Wade (2003).
Concerted simulations reveal how peroxidase compound III formation results in cellular oscillations.
  Biophys J, 85, 1421-1428.  
12001230 M.Falconi, L.Parrilli, A.Battistoni, and A.Desideri (2002).
Flexibility in monomeric Cu,Zn superoxide dismutase detected by limited proteolysis and molecular dynamics simulation.
  Proteins, 47, 513-520.  
11371434 M.Falconi, M.E.Stroppolo, P.Cioni, G.Strambini, A.Sergi, M.Ferrario, and A.Desideri (2001).
Dynamics-function correlation in Cu, Zn superoxide dismutase: a spectroscopic and molecular dynamics simulation study.
  Biophys J, 80, 2556-2567.  
  9828001 F.Polticelli, A.Battistoni, P.O'Neill, G.Rotilio, and A.Desideri (1998).
Role of the electrostatic loop charged residues in Cu,Zn superoxide dismutase.
  Protein Sci, 7, 2354-2358.  
  9423860 K.E.Wilks, K.L.Dunn, J.L.Farrant, K.M.Reddin, A.R.Gorringe, P.R.Langford, and J.S.Kroll (1998).
Periplasmic superoxide dismutase in meningococcal pathogenicity.
  Infect Immun, 66, 213-217.  
9600896 R.C.Wade, R.R.Gabdoulline, S.K.Lüdemann, and V.Lounnas (1998).
Electrostatic steering and ionic tethering in enzyme-ligand binding: insights from simulations.
  Proc Natl Acad Sci U S A, 95, 5942-5949.  
9294870 C.L.Fisher, D.E.Cabelli, R.A.Hallewell, P.Beroza, T.P.Lo, E.D.Getzoff, and J.A.Tainer (1997).
Computational, pulse-radiolytic, and structural investigations of lysine-136 and its role in the electrostatic triad of human Cu,Zn superoxide dismutase.
  Proteins, 29, 103-112.
PDB code: 1fun
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.