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PDBsum entry 1b06

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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
1b06
Jmol
Contents
Protein chains
(+ 0 more) 208 a.a. *
Metals
_FE ×6
Waters ×321
* Residue conservation analysis
PDB id:
1b06
Name: Oxidoreductase
Title: Superoxide dismutase from sulfolobus acidocaldarius
Structure: Protein (superoxide dismutase). Chain: a, b, c, d, e, f. Ec: 1.15.1.1
Source: Sulfolobus acidocaldarius. Organism_taxid: 330779. Strain: dsm 639. Atcc: dsm 639. Collection: dsm 639. Cellular_location: cytosol. Other_details: german collection of microorganisms
Biol. unit: Tetramer (from PDB file)
Resolution:
2.20Å     R-factor:   0.174     R-free:   0.223
Authors: S.Knapp,S.Kardinahl,H.Niklas,G.Tibbelin,G.Schafer,R.Ladenste
Key ref:
S.Knapp et al. (1999). Refined crystal structure of a superoxide dismutase from the hyperthermophilic archaeon Sulfolobus acidocaldarius at 2.2 A resolution. J Mol Biol, 285, 689-702. PubMed id: 9878438 DOI: 10.1006/jmbi.1998.2344
Date:
16-Nov-98     Release date:   18-Nov-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q08713  (SODF_SULAC) -  Superoxide dismutase [Fe]
Seq:
Struc:
211 a.a.
208 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: Iron or manganese or (zinc and copper)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1006/jmbi.1998.2344 J Mol Biol 285:689-702 (1999)
PubMed id: 9878438  
 
 
Refined crystal structure of a superoxide dismutase from the hyperthermophilic archaeon Sulfolobus acidocaldarius at 2.2 A resolution.
S.Knapp, S.Kardinahl, N.Hellgren, G.Tibbelin, G.Schäfer, R.Ladenstein.
 
  ABSTRACT  
 
The extremely thermostable superoxide dismutase from the hyperthermophilic archaeon Sulfolobus acidocaldarius was crystallized and the three-dimensional structure was determined by X-ray diffraction methods. The enzyme crystallized in the monoclinic spacegroup C2 with the cell dimensions a=168.1 A, b=91.3 A, c=85.7 A, beta=91.4 degrees. The diffraction limit of these crystals was 2.2 A. The crystals were very stable in the X-ray beam and measured diffraction data of a single crystal had a completeness of 99.5 % up to a resolution of 2.2 A.The crystal structure of S. acidocaldarius superoxide dismutase was solved by Patterson search methods using a dimer of Thermus thermophilus superoxide dismutase as a search model. The asymmetric unit accommodates three dimers. Two dimers form a tetramer by using only local symmetries; the third dimer forms a tetramer as well, however, by using the crystallographic 2-fold symmetry.The three-dimensional structure of the S. acidocaldarius dismutase has typical features of tetrameric dismutases. Secondary structure elements as well as residues important for the catalytic activity of the enzyme were found to be highly conserved. The model was refined at a resolution of 2.2 A and yielded a crystallographic R-value of 17.4 % (Rfree=22.3 %). A structural comparison of the two extremely stable tetrameric dismutases from S. acidocaldarius and Aquifex pyrophilus with the less stable enzyme from T. thermophilus and Mycoplasma tuberculosis revealed the structural determinants which are probably responsible for the high intrinsic stability of S. acidocaldarius dismutase. The most obvious factor which may give rise to the extraordinary thermal stability of S. acidocaldarius dismutase (melting temperature of about 125 degreesC) is the increase in intersubunit ion pairs and hydrogen bonds and, more importantly, the significant reduction of solvent-accessible hydrophobic surfaces, as well as an increase in the percentage of buried hydrophobic residues.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stereo pair of the crystal packing of SA-SOD in spacegroup C 2. Each asymmetric unit accommodates three dimers. The dimer in the asymmetric unit forms a tetramer using the crystallographic symmetry. The red and the blue colored aggregates (each six monomers) form one tetramer with crystallographic symmetry in between the dimers by contributing one dimer colored in red and one in blue.
Figure 7.
Figure 7. Active site of SA-SOD. (a) Sixfold averaged 2(F[o] -F[c]) exp ia[c] electron density map at the active site. The density of the OH - ligand is clearly visible. (b) Coordination of the iron atom. Bond lengths were averaged over the six monomers in the asymmetric unit. (c) Environment of the active site. (a) was generated using the program O [Jones and Kjeldgaard 1991]; (b) and (c) were drawn using the program RIBBON [Carlson 1991].
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 285, 689-702) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20972560 H.Xiang, G.Pan, C.R.Vossbrinck, R.Zhang, J.Xu, T.Li, Z.Zhou, C.Lu, and Z.Xiang (2010).
A Tandem Duplication of Manganese Superoxide Dismutase in Nosema bombycis and Its Evolutionary Origins.
  J Mol Evol, 71, 401-414.  
20491485 K.Ratcliff, and S.Marqusee (2010).
Identification of residual structure in the unfolded state of ribonuclease H1 from the moderately thermophilic Chlorobium tepidum: comparison with thermophilic and mesophilic homologues.
  Biochemistry, 49, 5167-5175.  
  20885930 T.Iwasaki (2010).
Iron-sulfur world in aerobic and hyperthermoacidophilic archaea Sulfolobus.
  Archaea, 2010, 0.  
  19193992 H.L.Pedersen, N.P.Willassen, and I.Leiros (2009).
The first structure of a cold-adapted superoxide dismutase (SOD): biochemical and structural characterization of iron SOD from Aliivibrio salmonicida.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 84-92.
PDB code: 2w7w
19408959 K.Ratcliff, J.Corn, and S.Marqusee (2009).
Structure, stability, and folding of ribonuclease H1 from the moderately thermophilic Chlorobium tepidum: comparison with thermophilic and mesophilic homologues.
  Biochemistry, 48, 5890-5898.
PDB code: 3h08
19229500 N.N.Song, Y.Zheng, S.J.E, and D.C.Li (2009).
Cloning, expression, and characterization of thermostable Manganese superoxide dismutase from Thermoascus aurantiacus var. levisporus.
  J Microbiol, 47, 123-130.  
20054483 S.Wang, Y.B.Yan, and Z.Y.Dong (2009).
Contributions of the C-Terminal Helix to the Structural Stability of a Hyperthermophilic Fe-Superoxide Dismutase (TcSOD).
  Int J Mol Sci, 10, 5498-5512.  
17420576 S.E, F.Guo, S.Liu, J.Chen, Y.Wang, and D.Li (2007).
Purification, characterization, and molecular cloning of a thermostable superoxide dismutase from Thermoascus aurantiacus.
  Biosci Biotechnol Biochem, 71, 1090-1093.  
17327673 S.Yoshikawa, R.Arai, Y.Kinoshita, T.Uchikubo-Kamo, T.Wakamatsu, R.Akasaka, R.Masui, T.Terada, S.Kuramitsu, M.Shirouzu, and S.Yokoyama (2007).
Structure of archaeal glyoxylate reductase from Pyrococcus horikoshii OT3 complexed with nicotinamide adenine dinucleotide phosphate.
  Acta Crystallogr D Biol Crystallogr, 63, 357-365.
PDB codes: 2dbq 2dbr 2dbz
17262208 Y.Z.He, K.Q.Fan, C.J.Jia, Z.J.Wang, W.B.Pan, L.Huang, K.Q.Yang, and Z.Y.Dong (2007).
Characterization of a hyperthermostable Fe-superoxide dismutase from hot spring.
  Appl Microbiol Biotechnol, 75, 367-376.  
16759231 M.Karlström, I.H.Steen, D.Madern, A.E.Fedöy, N.K.Birkeland, and R.Ladenstein (2006).
The crystal structure of a hyperthermostable subfamily II isocitrate dehydrogenase from Thermotoga maritima.
  FEBS J, 273, 2851-2868.
PDB code: 1zor
15290327 D.C.Li, J.Gao, Y.L.Li, and J.Lu (2005).
A thermostable manganese-containing superoxide dismutase from the thermophilic fungus Thermomyces lanuginosus.
  Extremophiles, 9, 1-6.  
16080154 K.Miyazono, Y.Sawano, and M.Tanokura (2005).
Crystal structure and structural stability of acylphosphatase from hyperthermophilic archaeon Pyrococcus horikoshii OT3.
  Proteins, 61, 196-205.  
14563869 T.Amo, H.Atomi, and T.Imanaka (2003).
Biochemical properties and regulated gene expression of the superoxide dismutase from the facultatively aerobic hyperthermophile Pyrobaculum calidifontis.
  J Bacteriol, 185, 6340-6347.  
12837801 X.Wang, X.He, S.Yang, X.An, W.Chang, and D.Liang (2003).
Structural basis for thermostability of beta-glycosidase from the thermophilic eubacterium Thermus nonproteolyticus HG102.
  J Bacteriol, 185, 4248-4255.
PDB code: 1np2
12382287 C.Charron, B.Vitoux, and A.Aubry (2002).
Comparative analysis of thermoadaptation within the archaeal glyceraldehyde-3-phosphate dehydrogenases from mesophilic Methanobacterium bryantii and thermophilic Methanothermus fervidus.
  Biopolymers, 65, 263-273.  
12392545 T.Hunter, J.V.Bannister, and G.J.Hunter (2002).
Thermostability of manganese- and iron-superoxide dismutases from Escherichia coli is determined by the characteristic position of a glutamine residue.
  Eur J Biochem, 269, 5137-5148.  
11238984 C.Vieille, and G.J.Zeikus (2001).
Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability.
  Microbiol Mol Biol Rev, 65, 1.  
11248699 E.De Vendittis, T.Ursby, R.Rullo, M.A.Gogliettino, M.Masullo, and V.Bocchini (2001).
Phenylmethanesulfonyl fluoride inactivates an archaeal superoxide dismutase by chemical modification of a specific tyrosine residue. Cloning, sequencing and expression of the gene coding for Sulfolobus solfataricus superoxide dismutase.
  Eur J Biochem, 268, 1794-1801.  
11141052 R.A.Edwards, M.M.Whittaker, J.W.Whittaker, E.N.Baker, and G.B.Jameson (2001).
Outer sphere mutations perturb metal reactivity in manganese superoxide dismutase.
  Biochemistry, 40, 15-27.
PDB codes: 1en4 1en5 1en6
11294629 R.A.Edwards, M.M.Whittaker, J.W.Whittaker, E.N.Baker, and G.B.Jameson (2001).
Removing a hydrogen bond in the dimer interface of Escherichia coli manganese superoxide dismutase alters structure and reactivity.
  Biochemistry, 40, 4622-4632.
PDB codes: 1i08 1i0h
10601872 R.Cannio, A.D'angelo, M.Rossi, and S.Bartolucci (2000).
A superoxide dismutase from the archaeon Sulfolobus solfataricus is an extracellular enzyme and prevents the deactivation by superoxide of cell-bound proteins.
  Eur J Biochem, 267, 235-243.  
11154067 S.Kardinahl, S.Anemüller, and G.Schäfer (2000).
The hyper-thermostable Fe-superoxide dismutase from the Archaeon Acidianus ambivalens: characterization, recombinant expression, crystallization and effects of metal exchange.
  Biol Chem, 381, 1089-1101.  
  10477309 G.Schäfer, M.Engelhard, and V.Müller (1999).
Bioenergetics of the Archaea.
  Microbiol Mol Biol Rev, 63, 570-620.  
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 code is shown on the right.