The crystal structure of an Fe-superoxide dismutase from the hyperthermophile Aquifex pyrophilus at 1.9 Å resolution: Structural basis for thermostability

Jae Hwan Lim, Yeon Gyu Yu, Ye Sun Han, Seung Je Cho, Byung Yoon Ahn, Sung Hou Kim, Yunje Cho

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118 Citations (Scopus)


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°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 Å 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 X-factor (I > 2σ) of 17.0% and X-free (I > 2σ) 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.

Original languageEnglish
Pages (from-to)259-274
Number of pages16
JournalJournal of Molecular Biology
Issue number2
Publication statusPublished - 1997 Jul 11

Bibliographical note

Funding Information:
We are grateful to Dr P. A. Karplus of Cornell University and Dr K.-S. Kim of KIST for their valuable comments, and Dr R. Kim of Lawrence Berkeley National Laboratory on the manuscript corrections, and Ms M. S. Koh of KIST for administrative help. This work was supported by grants from the Ministry of Science and Technology in Korea. S.-H. K. has been supported by the U.S. Department of Energy (DE-AC03-76SF00098). Coordinates used in this study were from the Brookhaven Data Bank. Ap SOD coordinates are being deposited with Brookhaven data bank. Meanwhile those interested may obtain the coordinates by request ( ).


  • Aquifex pyrophilus
  • Hyperthermophile
  • Ion-pair
  • Superoxide dismutase
  • Thermostability

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology


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