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PDBsum entry 3sod

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protein metals Protein-protein interface(s) links
Oxidoreductase (superoxide acceptor) PDB id
3sod
Jmol
Contents
Protein chains
152 a.a. *
Metals
_ZN ×4
_CU ×4
* Residue conservation analysis
PDB id:
3sod
Name: Oxidoreductase (superoxide acceptor)
Title: Changes in crystallographic structure and thermostability of a cu,zn superoxide dismutase mutant resulting from the removal of buried cysteine
Structure: Copper,zinc superoxide dismutase. Chain: o, y, g, b. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913
Resolution:
2.10Å     R-factor:   0.190    
Authors: D.E.Mcree,S.M.Redford,E.D.Getzoff,J.R.Lepock,R.A.Hallewell, J.A.Tainer
Key ref: D.E.McRee et al. (1990). Changes in crystallographic structure and thermostability of a Cu,Zn superoxide dismutase mutant resulting from the removal of a buried cysteine. J Biol Chem, 265, 14234-14241. PubMed id: 2387847
Date:
26-Jun-90     Release date:   15-Apr-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00442  (SODC_BOVIN) -  Superoxide dismutase [Cu-Zn]
Seq:
Struc:
152 a.a.
151 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!
  Cellular component     protein complex   11 terms 
  Biological process     reactive oxygen species metabolic process   45 terms 
  Biochemical function     antioxidant activity     10 terms  

 

 
    Added reference    
 
 
J Biol Chem 265:14234-14241 (1990)
PubMed id: 2387847  
 
 
Changes in crystallographic structure and thermostability of a Cu,Zn superoxide dismutase mutant resulting from the removal of a buried cysteine.
D.E.McRee, S.M.Redford, E.D.Getzoff, J.R.Lepock, R.A.Hallewell, J.A.Tainer.
 
  ABSTRACT  
 
In principle, protein thermostability depends on efficient interior packing of apolar residues and on avoidance of irreversible denaturation in the unfolded state. To study these effects, the single free cysteine in the highly stable enzyme bovine Cu,Zn superoxide dismutase was mutated to alanine (Cys6----Ala), and the recombinant protein was expressed in yeast, purified, characterized for reversible and irreversible denaturation, crystallized isomorphously to the wild-type enzyme, and used to determine the atomic structure. Removal of the chemically reactive thiol significantly decreased the rate of irreversible denaturation (as monitored by thermal inactivation at 70 degrees C), but the observed energetic cost (delta delta G of 0.7-1.3 kcal/mol as determined by differential scanning calorimetry) was much less than predicted from either the change in hydrophobicity or packing due to removal of the interior sulfur atom. X-ray diffraction data were collected to 2.1-A resolution using an area detector, and the atomic model for the mutant enzyme was determined by fitting to electron density difference maps, followed by reciprocal space refinement both with stereochemical restraints using PROLSQ and with molecular dynamics using X-PLOR. The refined 2.1-A resolution crystallographic structure suggests that small concerted and compensating shifts (less than 0.5 A) of the surrounding side chains and of the adjacent N- and C-terminal beta-strands significantly reduced the energetic cost of the interior mutation by improving packing and stereochemistry in the mutant enzyme. Taken together, these results differentiate between the effects of reversible and irreversible processes as they impact the design of thermostable proteins and suggest that relatively subtle concerted shifts can significantly reduce the energetic cost of evolutionary variation in internal residues of proteins with Greek key beta-barrel folds.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21110786 L.Foit, A.Mueller-Schickert, B.S.Mamathambika, S.Gleiter, C.L.Klaska, G.Ren, and J.C.Bardwell (2011).
Genetic selection for enhanced folding in vivo targets the cys14-cys38 disulfide bond in bovine pancreatic trypsin inhibitor.
  Antioxid Redox Signal, 14, 973-984.  
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
18645238 M.Yogavel, P.C.Mishra, J.Gill, P.K.Bhardwaj, S.Dutt, S.Kumar, P.S.Ahuja, and A.Sharma (2008).
Structure of a superoxide dismutase and implications for copper-ion chelation.
  Acta Crystallogr D Biol Crystallogr, 64, 892-901.  
17549562 C.F.Ken, C.T.Lin, Y.D.Wen, and J.L.Wu (2007).
Replacement of buried cysteine from zebrafish Cu/Zn superoxide dismutase and enhancement of its stability via site-directed mutagenesis.
  Mar Biotechnol (NY), 9, 335-342.  
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.  
15784978 K.Yamamoto, P.Zhang, Y.Banno, H.Fujii, F.Miake, N.Kashige, and Y.Aso (2005).
Superoxide dismutase from the silkworm, Bombyx mori: sequence, distribution, and overexpression.
  Biosci Biotechnol Biochem, 69, 507-514.  
16306691 Y.Tatara, T.Yoshida, and E.Ichishima (2005).
A single free cysteine residue and disulfide bond contribute to the thermostability of Aspergillus saitoi 1,2-alpha-mannosidase.
  Biosci Biotechnol Biochem, 69, 2101-2108.  
15367592 M.N.Becker, W.B.Greenleaf, D.A.Ostrov, and R.W.Moyer (2004).
Amsacta moorei entomopoxvirus expresses an active superoxide dismutase.
  J Virol, 78, 10265-10275.  
12149129 I.Fremaux, S.Mazères, A.Brisson-Lougarre, M.Arnaud, C.Ladurantie, and D.Fournier (2002).
Improvement of Drosophila acetylcholinesterase stability by elimination of a free cysteine.
  BMC Biochem, 3, 21.  
  10548053 N.Nagano, E.G.Hutchinson, and J.M.Thornton (1999).
Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels.
  Protein Sci, 8, 2072-2084.  
10194327 S.A.Potekhin, O.I.Loseva, E.I.Tiktopulo, and A.P.Dobritsa (1999).
Transition state of the rate-limiting step of heat denaturation of Cry3A delta-endotoxin.
  Biochemistry, 38, 4121-4127.  
9718300 L.Banci, M.Benedetto, I.Bertini, R.Del Conte, M.Piccioli, and M.S.Viezzoli (1998).
Solution structure of reduced monomeric Q133M2 copper, zinc superoxide dismutase (SOD). Why is SOD a dimeric enzyme?.
  Biochemistry, 37, 11780-11791.
PDB code: 1ba9
17029730 S.A.Potekhin, and E.L.Kovrigin (1998).
Folding under inequilibrium conditions as a possible reason for partial irreversibility of heat-denatured proteins: computer simulation study.
  Biophys Chem, 73, 241-248.  
8605177 G.E.Borgstahl, H.E.Parge, M.J.Hickey, M.J.Johnson, M.Boissinot, R.A.Hallewell, J.R.Lepock, D.E.Cabelli, and J.A.Tainer (1996).
Human mitochondrial manganese superoxide dismutase polymorphic variant Ile58Thr reduces activity by destabilizing the tetrameric interface.
  Biochemistry, 35, 4287-4297.
PDB code: 1var
8917495 Y.Bourne, S.M.Redford, H.M.Steinman, J.R.Lepock, J.A.Tainer, and E.D.Getzoff (1996).
Novel dimeric interface and electrostatic recognition in bacterial Cu,Zn superoxide dismutase.
  Proc Natl Acad Sci U S A, 93, 12774-12779.
PDB code: 1yai
7667303 P.B.Harbury, B.Tidor, and P.S.Kim (1995).
Repacking protein cores with backbone freedom: structure prediction for coiled coils.
  Proc Natl Acad Sci U S A, 92, 8408-8412.  
  7757009 T.P.Lo, M.E.Murphy, J.G.Guillemette, M.Smith, and G.D.Brayer (1995).
Replacements in a conserved leucine cluster in the hydrophobic heme pocket of cytochrome c.
  Protein Sci, 4, 198-208.
PDB codes: 1csu 1csv 1csw 1csx
  7920265 S.Bromberg, and K.A.Dill (1994).
Side-chain entropy and packing in proteins.
  Protein Sci, 3, 997.  
8038390 S.T.Ferreira, L.Stella, and E.Gratton (1994).
Conformational dynamics of bovine Cu, Zn superoxide dismutase revealed by time-resolved fluorescence spectroscopy of the single tyrosine residue.
  Biophys J, 66, 1185-1196.  
8278404 W.A.Lim, A.Hodel, R.T.Sauer, and F.M.Richards (1994).
The crystal structure of a mutant protein with altered but improved hydrophobic core packing.
  Proc Natl Acad Sci U S A, 91, 423-427.
PDB code: 1lli
8058892 F.M.Richards, and W.A.Lim (1993).
An analysis of packing in the protein folding problem.
  Q Rev Biophys, 26, 423-498.  
8436140 M.E.Schininà, F.Bossa, A.Lania, C.R.Capo, P.Carlini, and L.Calabrese (1993).
The primary structure of turtle Cu,Zn superoxide dismutase. Structural and functional irrelevance of an insert conferring proteolytic susceptibility.
  Eur J Biochem, 211, 843-849.  
7763513 V.V.Mozhaev (1993).
Mechanism-based strategies for protein thermostabilization.
  Trends Biotechnol, 11, 88-95.  
1518925 D.Shortle (1992).
Mutational studies of protein structures and their stabilities.
  Q Rev Biophys, 25, 205-250.  
1394426 G.E.Borgstahl, H.E.Parge, M.J.Hickey, W.F.Beyer, R.A.Hallewell, and J.A.Tainer (1992).
The structure of human mitochondrial manganese superoxide dismutase reveals a novel tetrameric interface of two 4-helix bundles.
  Cell, 71, 107-118.
PDB codes: 1abm 1n0j
1463506 H.E.Parge, R.A.Hallewell, and J.A.Tainer (1992).
Atomic structures of wild-type and thermostable mutant recombinant human Cu,Zn superoxide dismutase.
  Proc Natl Acad Sci U S A, 89, 6109-6113.
PDB code: 1sos
1367679 J.A.Tainer, V.A.Roberts, and E.D.Getzoff (1991).
Metal-binding sites in proteins.
  Curr Opin Biotechnol, 2, 582-591.  
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.