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J. Biol. Chem., Vol. 280, Issue 24, 22962-22967, June 17, 2005

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Crystal Structure of Human Vacuolar Protein Sorting Protein 29 Reveals a Phosphodiesterase/Nuclease-like Fold and Two Protein-Protein Interaction Sites^*

Deqiang Wang¶, Min Guo¶, Zhi Liang¶, Jun Fan¶, Zhiqiang Zhu¶, Jianye Zang¶, Zhongliang Zhu¶, Xiaowu Li¶, Maikun Teng¶||, Liwen Niu¶**, Yuhui Dong, and Peng Liu

From the Hefei National Laboratory of Physical Sciences at Microscale, Key Laboratory of Structural Biology of Chinese Academy of Sciences, the ^¶Department of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, and the Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Beijing 100039, China

Vacuolar protein sorting protein 29 (Vps29p), which is involved in retrograde trafficking from prevacuolar endosomes to the trans-Golgi network, performs its biological functions by participating in the formation of a "retromer complex." In human cells, this complex comprises four conserved proteins: hVps35p, hVps29p, hVps26p, and sorting nexin 1 protein (SNX1). Here, we report the crystal structure of hVps29p at 2.1 Å resolution, the first three-dimensional structure of the retromer subunits. This novel structure adopts a four-layered --- sandwich fold. hVps29p contains a metal-binding site that is very similar to the active sites of some proteins of the phosphodiesterase/nuclease protein family, indicating that hVps29p may carry out chemically similar functions. Structure and sequence conservation analysis suggests that hVps29p contains two protein-protein interaction sites. One site, which potentially serves as the interface between hVps29p and hVps35p, comprises 5 conserved hydrophobic and 8 hydrophilic residues. The other site is relatively more hydrophilic and may serve as a binding interface with hVps26p, SNX1, or other target proteins.

Received for publication, January 13, 2005 , and in revised form, March 14, 2005.

^* This work was supported by research grants from the Chinese National Natural Science Foundation (Grants 30121001, 30025012, and 30130080) (to L. N. and M. T.), the "973" and "863" Plans of the Chinese Ministry of Science and Technology (Grants G1999075603 and 2002BA711A13) (to L. N. and M. T.), and the Chinese Academy of Sciences (Grant KSCX1-SW-17) (to L. N. and M. T.). 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.

The atomic coordinates and structure factors (code 1W24) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

^|| To whom correspondence may be addressed. Tel.: 00-86-551-3606334; Fax: 00-86-551-3603046; E-mail: mkteng{at}ustc.edu.cn. ** To whom correspondence may be addressed. Tel.: 00-86-551-3606334; Fax: 00-86-551-3603046; E-mail: lwniu{at}ustc.edu.cn.

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