Table of Contents
Journal of Biophysics
Volume 2009, Article ID 434038, 12 pages
Research Article

Crystal Structural and Functional Analysis of the Putative Dipeptidase from Pyrococcus horikoshii OT3

1Experimental Facility Division, SPring-8 Group, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Hsinchu Science Park, Taiwan
2Peptide Institute, Inc., Ina Mino-shi, Osaka 562-8686, Japan
3RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
4RIKEN Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
5Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan

Received 3 February 2009; Accepted 30 April 2009

Academic Editor: Eaton Edward Lattman

Copyright © 2009 Jeyaraman Jeyakanthan et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


The crystal structure of a putative dipeptidase (Phdpd) from Pyrococcus horikoshii OT3 was solved using X-ray data at 2.4 Å resolution. The protein is folded into two distinct entities. The N-terminal domain consists of the general topology of the / fold, and the C-terminal domain consists of five long mixed strands, four helices, and two helices. The structure of Phdpd is quite similar to reported structures of prolidases from P. furiosus (Zn-Pfprol) and P. horikoshii (Zn-Phdpd), where Zn ions are observed in the active site resulting in an inactive form. However, Phdpd did not contain metals in the crystal structure and showed prolidase activity in the absence of additional Co ions, whereas the specific activities increased by 5 times in the presence of a sufficient concentration (1.2 mM) of Co ions. The substrate specificities (X-Pro) of Phdpd were broad compared with those of Zn-Phdpd in the presence of Co ions, whose relative activities are 10% or less for substrates other than Met-Pro, which is the most favorable substrate. The binding constants of Zn-Phdpd with three metals (Zn, Co, and Mn) were higher than those of Phdpd and that with Zn was higher by greater than 2 orders, which were determined by DSC experiments. From the structural comparison of both forms and the above experimental results, it could be elucidated why the protein with ions is inactive.