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PDBsum entry 1xm2

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Hydrolase PDB id
1xm2
Jmol
Contents
Protein chains
(+ 0 more) 149 a.a.
Ligands
SO4 ×6
Waters ×92

References listed in PDB file
Key reference
Title Trimeric structure of prl-1 phosphatase reveals an active enzyme conformation and regulation mechanisms.
Authors D.G.Jeong, S.J.Kim, J.H.Kim, J.H.Son, M.R.Park, S.M.Lim, T.S.Yoon, S.E.Ryu.
Ref. J Mol Biol, 2005, 345, 401-413. [DOI no: 10.1016/j.jmb.2004.10.061]
PubMed id 15571731
Abstract
The PRL phosphatases, which constitute a subfamily of the protein tyrosine phosphatases (PTPs), are implicated in oncogenic and metastatic processes. Here, we report the crystal structure of human PRL-1 determined at 2.7A resolution. The crystal structure reveals the shallow active-site pocket with highly hydrophobic character. A structural comparison with the previously determined NMR structure of PRL-3 exhibits significant differences in the active-site region. In the PRL-1 structure, a sulfate ion is bound to the active-site, providing stabilizing interactions to maintain the canonically found active conformation of PTPs, whereas the NMR structure exhibits an open conformation of the active-site. We also found that PRL-1 forms a trimer in the crystal and the trimer exists in the membrane fraction of cells, suggesting the possible biological regulation of PRL-1 activity by oligomerization. The detailed structural information on the active enzyme conformation and regulation of PRL-1 provides the structural basis for the development of potential inhibitors of PRL enzymes.
Figure 3.
Figure 3. Active-site. (a) Electron density map: the 2F[o] -F[c] electron density map around the PRL-1 active-site is presented in stereo as superposed with the refined structure. The electron density map is contoured at 1s level. (b) Comparison with VHR: active sites of PRL-1 (cyan) and VHR (magenta) were superposed and presented as worm models. PRL-1 residues (gold) are labeled as black and VHR residues (gray) are labeled as red. (c) Comparison with PRL-3 active-site of PRL-1 (cyan) and PRL-3 (gray) were superposed and presented as worm models. PRL-1 residues (gold) are labeled as black and PRL-3 residues (green) are labeled as red.
Figure 4.
Figure 4. Surface characteristics. (a) and (b) Sequence similarity between PRL-1 and PRL-3 is mapped onto the PRL-1 surface. The 100% identical, similar and different residue properties, as defined by the program ALSCRIPT37 are colored white, green and cyan, respectively. The active-site surface and the opposite surface are presented in (a) and (b), respectively. (c) and (d) Electrostatic potential surfaces of PRL-1 (c) and VHR (d) are presented. Positive and negative potentials are colored blue and red, respectively. The point of view is the same as (a). Residues near the active-site are labeled.
The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 345, 401-413) copyright 2005.
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