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Published online before print March 7, 2006
Protein Science, DOI: 10.1110/ps.052037006
 Copyright © 2006 The Protein Society
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Protein Structure Report

Crystal structure of Homo sapiens PTD012 revealsa zinc-containing hydrolase fold

Babu A. Manjasetty1,2,7, Konrad Bössow4,5, Martin Fieber-Erdmann1,3, Yvette Roske2,4, Johan Gobom5, Christoph Scheich4,5, Frank Götz2,4, Frank H. Niesen4,6 and Udo Heinemann2,3

1 Protein Structure Factory, Berlin 12489, Germany
2 Max-Delbrück-Centrum für Molekulare Medizin, Berlin 13092, Germany
3 Institut für Chemie und Biochemie, Berlin 14195, Germany
4 Protein Structure Factory, Berlin 14059, Germany
5 Max-Planck-Institut für Molekulare Genetik, Berlin 14195, Germany
6 Institut für Medizinische Physik und Biophysik, Charité Universitätsmedizin Berlin, Berlin 10098, Germany

(RECEIVED December 13, 2005; FINAL REVISION December 13, 2005; ACCEPTED December 16, 2005)

The human protein PTD012 is the longer product of an alternatively spliced gene and was described to be localized in the nucleus. The X-ray structure analysis at 1.7 Å resolution of PTD012 through SAD phasing reveals a monomeric protein and a novel fold. The shorter splice form was also studied and appears to be unfolded and non-functional. The structure of PTD012 displays an {alpha}betabeta{alpha} four-layer topology. A metal ion residing between the central beta-sheets is partially coordinated by three histidine residues. X-ray absorption near-edge structure (XANES) analysis identifies the PTD012-bound ion as Zn2+. Tetrahedral coordination of the ion is completed by the carboxylate oxygen atom of an acetate molecule taken up fromthe crystallization buffer. The binding of Zn2+ to PTD012 is reminiscent of zinccontaining enzymes such as carboxypeptidase, carbonic anhydrase, and beta-lactamase. Biochemical assays failed to demonstrate any of these enzyme activities in PTD012. However, PTD012 exhibits ester hydrolase activity on the substrate p-nitrophenyl acetate.

Keywords: PTD012 family; alternative splicing; splice variant; structural genomics; Zn-binding site; ester hydrolase

7 Present address: Case Center for Proteomics, Case Western Reserve University, Upton, NY 11973, USA.

Reprint requests to: Udo Heinemann, Max Delbrück Center for Molecular Medicine Robert-Rössle-Str. 10 D-13092, Berlin, Germany; e-mail heinemann{at}mdc-berlin.de; fax: +49-30-9406-2548.

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.052037006

Supplementary material: see www.proteinscience.org


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