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J. Biol. Chem., Vol. 282, Issue 6, 3856-3863, February 9, 2007

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Solution Structure and Backbone Dynamics of an Endopeptidase HycI from scherichia coli

IMPLICATIONS FOR MECHANISM OF THE [NiFe] HYDROGENASE MATURATION^*

Fan Yang, Wei Hu^¶, Huimin Xu^¶, Congmin Li¹, Bin Xia^¶, and Changwen Jin^¶2

From the Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and ^¶College of Life Sciences, Peking University, Beijing 100871, China

[NiFe] hydrogenases are metalloenzymes involved in many biological processes concerning the metabolism of hydrogen. The maturation of the large subunit of these hydrogenases requires the cleavage of a peptide at the C terminus by an endopeptidase before the final formation of the [NiFe] metallocenter. HycI is an endopeptidase of the M52 family and responsible for the C-terminal cleavage of the large subunit of hydrogenase 3 in Escherichia coli. Although extensive studies were performed, the molecular mechanism of recognition and cleavage of hydrogenase 3 remains elusive. Herein, we report the solution structure of E. coli HycI determined by high resolution nuclear magnetic resonance spectroscopy. This is the first solution structure of the apo form of endopeptidase of the M52 family reported thus far. The overall structure is similar to the crystal structure of holo-HybD in the same family. However, significant diversity was observed between the two structures. Especially, HycI shows an open conformation at the putative nickel-binding site, whereas HybD adopts a closed conformation. In addition, we performed backbone dynamic studies to probe the motional properties of the apo form of HycI. Furthermore, the metal ion titration experiments provide insightful information on the substrate recognition and cleavage processes. Taken together, our current structural, biochemical, and dynamic studies extend the knowledge of the M52 family proteins and provide novel insights into the biological function of HycI.

Received for publication, September 29, 2006 , and in revised form, November 20, 2006.

The atomic coordinates and structure factors (code 2I8L) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

^* This work was supported by National Natural Science Foundation of China Grants 30125009 (to B. X.), 30570354 (to C. J.), and 30325010 (to C. J.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

¹ Present address: Dept. of Chemistry, University of California, Davis, One Shields Ave., Davis, CA 95616.

² To whom correspondence should be addressed. Tel.: 86-6275-6004; Fax: 86-6275-3790; E-mail: changwen{at}pku.edu.cn.

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