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PDBsum entry 2jcw

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protein metals links
Oxidoreductase PDB id
2jcw
Jmol
Contents
Protein chain
153 a.a. *
Metals
_ZN
CU1
Waters ×109
* Residue conservation analysis
PDB id:
2jcw
Name: Oxidoreductase
Title: Reduced bridge-broken yeast cu/zn superoxide dismutase room temperature (298k) structure
Structure: Cu/zn superoxide dismutase. Chain: a. Synonym: yeast cu/zn sod. Other_details: room (298k) temperature structure with the copper-imidazolate bridge broken
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Cellular_location: cytoplasm. Other_details: carlbiotech, copenhagen
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
1.70Å     R-factor:   0.191    
Authors: P.J.Hart,M.M.Balbirnie,N.L.Ogihara,A.M.Nersissian,M.S.Weiss, J.S.Valentine,D.Eisenberg
Key ref:
P.J.Hart et al. (1999). A structure-based mechanism for copper-zinc superoxide dismutase. Biochemistry, 38, 2167-2178. PubMed id: 10026301 DOI: 10.1021/bi982284u
Date:
21-Dec-98     Release date:   08-Jun-99    
Supersedes: 1jcw
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00445  (SODC_YEAST) -  Superoxide dismutase [Cu-Zn]
Seq:
Struc:
154 a.a.
153 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     cytoplasm   5 terms 
  Biological process     positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress   11 terms 
  Biochemical function     antioxidant activity     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi982284u Biochemistry 38:2167-2178 (1999)
PubMed id: 10026301  
 
 
A structure-based mechanism for copper-zinc superoxide dismutase.
P.J.Hart, M.M.Balbirnie, N.L.Ogihara, A.M.Nersissian, M.S.Weiss, J.S.Valentine, D.Eisenberg.
 
  ABSTRACT  
 
A reaction cycle is proposed for the mechanism of copper-zinc superoxide dismutase (CuZnSOD) that involves inner sphere electron transfer from superoxide to Cu(II) in one portion of the cycle and outer sphere electron transfer from Cu(I) to superoxide in the other portion of the cycle. This mechanism is based on three yeast CuZnSOD structures determined by X-ray crystallography together with many other observations. The new structures reported here are (1) wild type under 15 atm of oxygen pressure, (2) wild type in the presence of azide, and (3) the His48Cys mutant. Final R-values for the three structures are respectively 20.0%, 17.3%, and 20.9%. Comparison of these three new structures to the wild-type yeast Cu(I)ZnSOD model, which has a broken imidazolate bridge, reveals the following: (i) The protein backbones (the "SOD rack") remain essentially unchanged. (ii) A pressure of 15 atm of oxygen causes a displacement of the copper ion 0.37 A from its Cu(I) position in the trigonal plane formed by His46, His48, and His120. The displacement is perpendicular to this plane and toward the NE2 atom of His63 and is accompanied by elongated copper electron density in the direction of the displacement suggestive of two copper positions in the crystal. The copper geometry remains three coordinate, but the His48-Cu bond distance increases by 0.18 A. (iii) Azide binding also causes a displacement of the copper toward His63 such that it moves 1.28 A from the wild-type Cu(I) position, but unlike the effect of 15 atm of oxygen, there is no two-state character. The geometry becomes five-coordinate square pyramidal, and the His63 imidazolate bridge re-forms. The His48-Cu distance increases by 0.70 A, suggesting that His48 becomes an axial ligand. (iv) The His63 imidazole ring tilts upon 15 atm of oxygen treatment and azide binding. Its NE2 atom moves toward the trigonal plane by 0.28 and 0.66 A, respectively, in these structures. (v) The replacement of His48 by Cys, which does not bind copper, results in a five-coordinate square pyramidal, bridge-intact copper geometry with a novel chloride ligand. Combining results from these and other CuZnSOD crystal structures, we offer the outlines of a structure-based cyclic mechanism.
 

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
21212887 T.Kawashima, K.Ohkubo, and S.Fukuzumi (2011).
Stepwise vs. concerted pathways in scandium ion-coupled electron transfer from superoxide ion to p-benzoquinone derivatives.
  Phys Chem Chem Phys, 13, 3344-3352.  
20333422 O.E.Johnson, K.C.Ryan, M.J.Maroney, and T.C.Brunold (2010).
Spectroscopic and computational investigation of three Cys-to-Ser mutants of nickel superoxide dismutase: insight into the roles played by the Cys2 and Cys6 active-site residues.
  J Biol Inorg Chem, 15, 777-793.  
19651777 A.Tiwari, A.Liba, S.H.Sohn, S.V.Seetharaman, O.Bilsel, C.R.Matthews, P.J.Hart, J.S.Valentine, and L.J.Hayward (2009).
Metal deficiency increases aberrant hydrophobicity of mutant superoxide dismutases that cause amyotrophic lateral sclerosis.
  J Biol Chem, 284, 27746-27758.  
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
19421792 Q.Lu, X.Li, Y.Wang, and G.Chen (2009).
Catalytic activities of dismution reactions of Cu(bpy)Br(2) compound and its derivatives as SOD mimics: a theoretical study.
  J Mol Model, 15, 1397-1405.  
19089529 Y.G.Gocheva, S.Tosi, E.T.Krumova, L.S.Slokoska, J.G.Miteva, S.V.Vassilev, and M.B.Angelova (2009).
Temperature downshift induces antioxidant response in fungi isolated from Antarctica.
  Extremophiles, 13, 273-281.  
18604568 C.Andreini, I.Bertini, G.Cavallaro, G.L.Holliday, and J.M.Thornton (2008).
Metal ions in biological catalysis: from enzyme databases to general principles.
  J Biol Inorg Chem, 13, 1205-1218.  
18040680 S.Raimondi, D.Uccelletti, D.Matteuzzi, U.M.Pagnoni, M.Rossi, and C.Palleschi (2008).
Characterization of the superoxide dismutase SOD1 gene of Kluyveromyces marxianus L3 and improved production of SOD activity.
  Appl Microbiol Biotechnol, 77, 1269-1277.  
18836000 S.Raimondi, E.Zanni, C.Talora, M.Rossi, C.Palleschi, and D.Uccelletti (2008).
SOD1, a new Kluyveromyces lactis helper gene for heterologous protein secretion.
  Appl Environ Microbiol, 74, 7130-7137.  
17150313 B.Dash, R.Metz, H.J.Huebner, W.Porter, and T.D.Phillips (2007).
Molecular characterization of two superoxide dismutases from Hydra vulgaris.
  Gene, 387, 93.  
17888947 B.R.Roberts, J.A.Tainer, E.D.Getzoff, D.A.Malencik, S.R.Anderson, V.C.Bomben, K.R.Meyers, P.A.Karplus, and J.S.Beckman (2007).
Structural characterization of zinc-deficient human superoxide dismutase and implications for ALS.
  J Mol Biol, 373, 877-890.
PDB code: 2r27
17405879 H.Yamasaki, S.E.Abdel-Ghany, C.M.Cohu, Y.Kobayashi, T.Shikanai, and M.Pilon (2007).
Regulation of copper homeostasis by micro-RNA in Arabidopsis.
  J Biol Chem, 282, 16369-16378.  
16291742 L.Banci, I.Bertini, F.Cantini, N.D'Amelio, and E.Gaggelli (2006).
Human SOD1 before harboring the catalytic metal: solution structure of copper-depleted, disulfide-reduced form.
  J Biol Chem, 281, 2333-2337.
PDB code: 2af2
17070679 Y.G.Gocheva, E.T.Krumova, L.S.Slokoska, J.G.Miteva, S.V.Vassilev, and M.B.Angelova (2006).
Cell response of Antarctic and temperate strains of Penicillium spp. to different growth temperature.
  Mycol Res, 110, 1347-1354.  
16440303 Y.H.Huang, C.M.Shih, C.J.Huang, C.M.Lin, C.M.Chou, M.L.Tsai, T.P.Liu, J.F.Chiu, and C.T.Chen (2006).
Effects of cadmium on structure and enzymatic activity of Cu,Zn-SOD and oxidative status in neural cells.
  J Cell Biochem, 98, 577-589.  
16220142 A.E.Bednarski, S.C.Elgin, and H.B.Pakrasi (2005).
An inquiry into protein structure and genetic disease: introducing undergraduates to bioinformatics in a large introductory course.
  Cell Biol Educ, 4, 207-220.  
16059957 A.Wada, S.Yamaguchi, K.Jitsukawa, and H.Masuda (2005).
Preparation of a hydroperoxo zinc(II) intermediate.
  Angew Chem Int Ed Engl, 44, 5698-5701.  
15952898 J.S.Valentine, P.A.Doucette, and S.Zittin Potter (2005).
Copper-zinc superoxide dismutase and amyotrophic lateral sclerosis.
  Annu Rev Biochem, 74, 563-593.  
15328354 F.Dupeyrat, C.Vidaud, A.Lorphelin, and C.Berthomieu (2004).
Long distance charge redistribution upon Cu,Zn-superoxide dismutase reduction: significance for dismutase function.
  J Biol Chem, 279, 48091-48101.  
15173586 J.Wuerges, J.W.Lee, Y.I.Yim, H.S.Yim, S.O.Kang, and K.Djinovic Carugo (2004).
Crystal structure of nickel-containing superoxide dismutase reveals another type of active site.
  Proc Natl Acad Sci U S A, 101, 8569-8574.
PDB codes: 1q0d 1q0f 1q0g 1q0k 1q0m
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
12485776 B.Ge, F.W.Scheller, and F.Lisdat (2003).
Electrochemistry of immobilized CuZnSOD and FeSOD and their interaction with superoxide radicals.
  Biosens Bioelectron, 18, 295-302.  
12906825 M.A.Hough, and S.S.Hasnain (2003).
Structure of fully reduced bovine copper zinc superoxide dismutase at 1.15 A.
  Structure, 11, 937-946.
PDB code: 1q0e
12926004 R.Prabhakar, and P.E.Siegbahn (2003).
A comparison of the mechanism for the reductive half-reaction between pea seedling and other copper amine oxidases (CAOs).
  J Comput Chem, 24, 1599-1609.  
11854284 L.J.Hayward, J.A.Rodriguez, J.W.Kim, A.Tiwari, J.J.Goto, D.E.Cabelli, J.S.Valentine, and R.H.Brown (2002).
Decreased metallation and activity in subsets of mutant superoxide dismutases associated with familial amyotrophic lateral sclerosis.
  J Biol Chem, 277, 15923-15931.  
11763463 H.Ohtsu, and S.Fukuzumi (2001).
Coordination of semiquinone and superoxide radical anions to the zinc ion in SOD model complexes that act as the key step in disproportionation of the radical anions.
  Chemistry, 7, 4947-4953.  
11717503 R.M.Cardoso, C.H.da Silva, A.P.de Araújo, T.Tanaka, M.Tanaka, and R.C.Garratt (2001).
Expression and preliminary X-ray diffraction studies of cytosolic Cu,Zn superoxide dismutase from Schistosoma mansoni.
  Acta Crystallogr D Biol Crystallogr, 57, 1877-1880.  
11169662 H.Ohtsu, and S.Fukuzumi (2000).
The Essential Role of a Zn(II) Ion in the Disproportionation of Semiquinone Radical Anion by an Imidazolate-Bridged Cu(II)-Zn(II) Model of Superoxide Dismutase We are grateful to Mituo Ohama, Graduate School of Science, Osaka University, for recording resonance Raman spectra. This work was partially supported by a Grant-in-Aid for Scientific Research Priority Area (No. 11228205) from the Ministry of Education, Science, Sports and Culture, Japan.
  Angew Chem Int Ed Engl, 39, 4537-4539.  
10858280 J.F.Eisses, J.P.Stasser, M.Ralle, J.H.Kaplan, and N.J.Blackburn (2000).
Domains I and III of the human copper chaperone for superoxide dismutase interact via a cysteine-bridged Dicopper(I) cluster.
  Biochemistry, 39, 7337-7342.  
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.