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Published online before print May 27, 2008, 10.1110/ps.035881.108
Protein Science (2008), 17:1362-1373. Published by Cold Spring Harbor Laboratory Press. Copyright © 2008 The Protein Society
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Crystal structure and mutagenic analysis of GDOsp, a gentisate 1,2-dioxygenase from Silicibacter Pomeroyi

Jia Chen1,7, Wei Li2,7, Mingzhu Wang1, Guangyu Zhu3, Dongqi Liu4, Fei Sun1, Ning Hao1, Xuemei Li1, Zihe Rao1,5,6, and Xuejun C. Zhang1,3

1 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
2 State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
3 Crystallography Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, USA
4 School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430064, China
5 Laboratory of Structural Biology, Tsinghua University, Beijing 100084, People's Republic of China
6 College of Life Sciences and Tianjin State Laboratory of Protein Sciences, Nankai University, Tianjin 300071, China

(RECEIVED April 18, 2008; FINAL REVISION May 14, 2008; ACCEPTED May 14, 2008)

Dioxygenases catalyze dioxygen incorporation into various organic compounds and play a key role in the complex degradation pathway of mono- and polycyclic aromatic and hetero-aromatic compounds. Here we report the crystal structure of gentisate 1,2-dioxygenase from Silicibacter pomeroyi (GDOsp) at a 2.8 Å resolution. The enzyme possessed a conserved three-dimensional structure of the bicupin family, forming a homotetramerization. However, each subunit of GDOsp unusually contained two ferrous centers that were located in its two homologous cupin domains, respectively. Further mutagenic analysis indicated that the enzyme activity of GDOsp depends on the microenvironment in both metal-binding sites. Moreover, homologous structural comparison and functional study on GDOsp variants unveiled a group of functionally essential residues and suggested that the active site of the enzyme is located in the amino-terminal domain, but could be influenced by changes in the carboxyl domain. Therefore, GDOsp may provide a working model for studying long-distance communication within a protein (or its complex).

Keywords: gentisate 1,2-dioxygenase; extradiol dioxygenase; mononuclear metal center; bicupin folding; long-distance communication


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