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PDBsum entry 1coj

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protein metals links
Oxidoreductase PDB id
1coj
Jmol
Contents
Protein chain
211 a.a. *
Metals
_FE
Waters ×102
* Residue conservation analysis
PDB id:
1coj
Name: Oxidoreductase
Title: Fe-sod from aquifex pyrophilus, a hyperthermophilic bacteriu
Structure: Protein (superoxide dismutase). Chain: a. Engineered: yes
Source: Aquifex pyrophilus. Organism_taxid: 2714. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Other_details: german collection of microorganisms (dsm)
Biol. unit: Homo-Tetramer (from PDB file)
Resolution:
1.90Å     R-factor:   0.170     R-free:   0.200
Authors: J.H.Lim,Y.G.Yu,S.-H.Kim,S.-J.Cho,B.Y.Ahn,Y.S.Han,Y.Cho
Key ref:
J.H.Lim et al. (1997). The crystal structure of an Fe-superoxide dismutase from the hyperthermophile Aquifex pyrophilus at 1.9 A resolution: structural basis for thermostability. J Mol Biol, 270, 259-274. PubMed id: 9236127 DOI: 10.1006/jmbi.1997.1105
Date:
28-May-99     Release date:   14-Jun-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9X6W9  (SODF_AQUPY) -  Superoxide dismutase [Fe]
Seq:
Struc:
213 a.a.
211 a.a.
Key:    PfamA domain  Secondary structure

 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!
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1006/jmbi.1997.1105 J Mol Biol 270:259-274 (1997)
PubMed id: 9236127  
 
 
The crystal structure of an Fe-superoxide dismutase from the hyperthermophile Aquifex pyrophilus at 1.9 A resolution: structural basis for thermostability.
J.H.Lim, Y.G.Yu, Y.S.Han, S.Cho, B.Y.Ahn, S.H.Kim, Y.Cho.
 
  ABSTRACT  
 
Superoxide dismutase (SOD) from Aquifex pyrophilus, a hyperthermophilic bacterium, is an extremely heat-stable enzyme that maintains about 70% of its activity after heat treatment for 60 minutes at 100 degrees C. To understand the molecular basis of thermostability of this enzyme, we have determined the crystal structure of A. pyrophilus superoxide dismutase (Ap SOD), an Fe containing homotetrameric enzyme, at 1.9 A resolution, and compared it with SOD structures from a mesophile and a thermophile, and other enzyme structures from other hyperthermophiles. The structure has been refined to a crystallographic R-factor (I > 2sigma) of 17.0% and R-free (I > 2sigma) of 19.9%. While the overall structure of the Ap SOD monomer is similar to the other SODs, significant conformational differences are observed in a highly variable loop region and the C-terminal helix. The conformational differences in these regions alter the subunit arrangement of this enzyme and generate a very compact tetramer. Structural comparisons of three SODs have revealed that Ap SOD has some stabilizing features at both the tertiary and the quaternary structural level: The Ap SOD monomer contains a large number of ion-pairs and the Ap SOD tetramer has a dramatically increased buried surface area per monomer. Comparisons of the Ap SOD structure with that of other known enzymes from hyperthermophiles reveal that the increased number of intrasubunit ion-pairs is a common feature.
 
  Selected figure(s)  
 
Figure 9.
Figure 9. (a) Stereodiagram showing the distributions of ion-pairs in the Ap SOD monomer. The negatively charged residues are shown in blue and the positively charged residues are shown in red. The metal ion is shown in yellow. (b) Stereodiagram of the intrasubunit ion-pair networks in the N terminus of Ap SOD. Residues in loop L1 and the a1 helix are involved in network formation.
Figure 10.
Figure 10. A space-filling model showing the intersubunit ion-pairs of the (a) Ap SOD, (b) Mt SOD, and (c) Tt SOD tetramer. Subunits A and D are yellow and B and C are white, and are labeled. The residues involved in the intersub- unit ion-pairs are shown in blue (negatively charged) and in red (positively charged).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 270, 259-274) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21331408 C.M.Yang (2011).
Biometal binding-site mimicry with modular, hetero-bifunctionally modified architecture encompassing a Trp/His motif: insights into spatiotemporal noncovalent interactions from a comparative spectroscopic study.
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21197558 J.Liu, M.Yin, H.Zhu, J.Lu, and Z.Cui (2011).
Purification and characterization of a hyperthermostable Mn-superoxide dismutase from Thermus thermophilus HB27.
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21340017 S.Areekit, P.Kanjanavas, P.Khawsak, A.Pakpitchareon, K.Potivejkul, G.Chansiri, and K.Chansiri (2011).
Cloning, Expression, and Characterization of Thermotolerant Manganese Superoxide Dismutase from Bacillus sp. MHS47.
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21182595 T.Nakamura, K.Torikai, K.Uegaki, J.Morita, K.Machida, A.Suzuki, and Y.Kawata (2011).
Crystal structure of the cambialistic superoxide dismutase from Aeropyrum pernix K1--insights into the enzyme mechanism and stability.
  FEBS J, 278, 598-609.
PDB codes: 3ak1 3ak2 3ak3
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.
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20607149 J.Jia, W.Chen, H.Ma, K.Wang, and C.Zhao (2010).
Use of a rhodamine-based bifunctional probe in N-terminal specific labeling of Thermomyces lanuginosus xylanase.
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  19886398 A.Valdivia, S.Pérez-Alvarez, J.D.Aroca-Aguilar, I.Ikuta, and J.Jordán (2009).
Superoxide dismutases: a physiopharmacological update.
  J Physiol Biochem, 65, 195-208.  
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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
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).
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17651440 K.Yoneda, H.Sakuraba, H.Tsuge, N.Katunuma, and T.Ohshima (2007).
Crystal structure of archaeal highly thermostable L-aspartate dehydrogenase/NAD/citrate ternary complex.
  FEBS J, 274, 4315-4325.
PDB code: 2dc1
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.  
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.  
15688447 H.K.Liang, C.M.Huang, M.T.Ko, and J.K.Hwang (2005).
Amino acid coupling patterns in thermophilic proteins.
  Proteins, 59, 58-63.  
15532068 C.H.Chan, H.K.Liang, N.W.Hsiao, M.T.Ko, P.C.Lyu, and J.K.Hwang (2004).
Relationship between local structural entropy and protein thermostability.
  Proteins, 57, 684-691.  
14573594 J.M.Choi, E.Y.Park, J.H.Kim, S.K.Chang, and Y.Cho (2004).
Probing the functional importance of the hexameric ring structure of RNase PH.
  J Biol Chem, 279, 755-764.
PDB codes: 1r6l 1r6m
  16233593 K.Shiraki, S.Nishikori, S.Fujiwara, T.Imanaka, and M.Takagi (2004).
Contribution of protein-surface ion pairs of a hyperthermophilic protein on thermal and thermodynamic stability.
  J Biosci Bioeng, 97, 75-77.  
14672935 R.Wintjens, C.Noël, A.C.May, D.Gerbod, F.Dufernez, M.Capron, E.Viscogliosi, and M.Rooman (2004).
Specificity and phenetic relationships of iron- and manganese-containing superoxide dismutases on the basis of structure and sequence comparisons.
  J Biol Chem, 279, 9248-9254.  
15340929 T.Akiba, M.Nishio, I.Matsui, and K.Harata (2004).
X-ray structure of a membrane-bound beta-glycosidase from the hyperthermophilic archaeon Pyrococcus horikoshii.
  Proteins, 57, 422-431.
PDB code: 1vff
14747705 Y.Maruyama, N.Maruyama, B.Mikami, and S.Utsumi (2004).
Structure of the core region of the soybean beta-conglycinin alpha' subunit.
  Acta Crystallogr D Biol Crystallogr, 60, 289-297.
PDB code: 1uik
12012341 B.Cobucci-Ponzano, M.Moracci, B.Di Lauro, M.Ciaramella, R.D'Avino, and M.Rossi (2002).
Ionic network at the C-terminus of the beta-glycosidase from the hyperthermophilic archaeon Sulfolobus solfataricus: Functional role in the quaternary structure thermal stabilization.
  Proteins, 48, 98.  
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.  
12057200 M.Comellas-Bigler, P.Fuentes-Prior, K.Maskos, R.Huber, H.Oyama, K.Uchida, B.M.Dunn, K.Oda, and W.Bode (2002).
The 1.4 a crystal structure of kumamolysin: a thermostable serine-carboxyl-type proteinase.
  Structure, 10, 865-876.
PDB codes: 1gt9 1gtg 1gtj 1gtl
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
10788490 G.Gonzalez-Blasco, J.Sanz-Aparicio, B.Gonzalez, J.A.Hermoso, and J.Polaina (2000).
Directed evolution of beta -glucosidase A from Paenibacillus polymyxa to thermal resistance.
  J Biol Chem, 275, 13708-13712.  
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.  
10848964 S.Sugio, B.Y.Hiraoka, and F.Yamakura (2000).
Crystal structure of cambialistic superoxide dismutase from porphyromonas gingivalis.
  Eur J Biochem, 267, 3487-3495.
PDB code: 1qnn
10383424 M.Alvarez, J.Wouters, D.Maes, V.Mainfroid, F.Rentier-Delrue, L.Wyns, E.Depiereux, and J.A.Martial (1999).
Lys13 plays a crucial role in the functional adaptation of the thermophilic triose-phosphate isomerase from Bacillus stearothermophilus to high temperatures.
  J Biol Chem, 274, 19181-19187.
PDB code: 2btm
10574944 M.M.Whittaker, and J.W.Whittaker (1999).
Thermally triggered metal binding by recombinant Thermus thermophilus manganese superoxide dismutase, expressed as the apo-enzyme.
  J Biol Chem, 274, 34751-34757.  
10206992 S.Y.Kim, K.Y.Hwang, S.H.Kim, H.C.Sung, Y.S.Han, and Y.Cho (1999).
Structural basis for cold adaptation. Sequence, biochemical properties, and crystal structure of malate dehydrogenase from a psychrophile Aquaspirillium arcticum.
  J Biol Chem, 274, 11761-11767.
PDB codes: 1b8p 1b8u 1b8v
9690987 F.T.Robb, and D.L.Maeder (1998).
Novel evolutionary histories and adaptive features of proteins from hyperthermophiles
  Curr Opin Biotechnol, 9, 288-291.  
9603906 F.Yamakura, H.Taka, T.Fujimura, and K.Murayama (1998).
Inactivation of human manganese-superoxide dismutase by peroxynitrite is caused by exclusive nitration of tyrosine 34 to 3-nitrotyrosine.
  J Biol Chem, 273, 14085-14089.  
9860869 K.Ogasahara, M.Nakamura, S.Nakura, S.Tsunasawa, I.Kato, T.Yoshimoto, and K.Yutani (1998).
The unusually slow unfolding rate causes the high stability of pyrrolidone carboxyl peptidase from a hyperthermophile, Pyrococcus furiosus: equilibrium and kinetic studies of guanidine hydrochloride-induced unfolding and refolding.
  Biochemistry, 37, 17537-17544.  
9712831 M.M.Whittaker, and J.W.Whittaker (1998).
A glutamate bridge is essential for dimer stability and metal selectivity in manganese superoxide dismutase.
  J Biol Chem, 273, 22188-22193.  
9893953 R.Scandurra, V.Consalvi, R.Chiaraluce, L.Politi, and P.C.Engel (1998).
Protein thermostability in extremophiles.
  Biochimie, 80, 933-941.  
9914255 U.Ermler, W.Grabarse, S.Shima, M.Goubeaud, and R.K.Thauer (1998).
Active sites of transition-metal enzymes with a focus on nickel.
  Curr Opin Struct Biol, 8, 749-758.  
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.