PDBsum entry 1urm

Antioxidant enzyme

PDB id: 1urm

Contents

Protein chain

162 a.a. *

Ligands

BEZ

Metals

_CL ×3

Waters ×285

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of the c47s mutant of human peroxiredoxin 5

Authors

C.Evrard, A.Smeets, B.Knoops, J.P.Declercq.

Ref.

J Chem Cryst, 2004, 34, 553.

Secondary reference #1

Title

Crystal structure of human peroxiredoxin 5, A novel type of mammalian peroxiredoxin at 1.5 a resolution.

Authors

J.P.Declercq, C.Evrard, A.Clippe, D.V.Stricht, A.Bernard, B.Knoops.

Ref.

J Mol Biol, 2001, 311, 751-759. [DOI no: 10.1006/jmbi.2001.4853]

PubMed id

11518528

Figure 1.
Figure 1. Overall view of the structure of PRDX5. (a) Topological diagram showing the arrangement of the secondary structural elements in PRDX5. The helices are represented as cylinders and the b-strands as arrows. The beginning and the end of the secondary structural elements are labelled. The three helices and the four b-strands belonging to the thioredoxin fold are colored green and red, respectively, while the remaining elements are colored yellow. (b) and (c) Ribbon diagrams showing the overall organization of PRDX5, colored as in (a). The two orientations are nearly perpendicular, (c) being a top view of (b). The side-chains of the three Cys residues are represented as balls and sticks (Cys72 is hidden in (b)). Parts (b) and (c) were prepared using MOLSCRIPT[26] and Raster3D. [27]

Figure 2.
Figure 2. Structural comparisons with other peroxiredoxins. Stereoscopic view of a superposition between the C^a traces of PRDX5 (red) and (a) hORF6, (b) HBP23 (green). The orientation is the same as in Figure 1(b). The Figures were produced using O. [13]

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #2

Title

A twinned monoclinic crystal form of human peroxiredoxin 5 with eight molecules in the asymmetric unit.

Authors

J.P.Declercq, C.Evrard.

Ref.

Acta Crystallogr D Biol Crystallogr, 2001, 57, 1829-1835. [DOI no: 10.1107/S0907444901015475]

PubMed id

11717495

Figure 2.
Figure 2 The self-rotation function after detwinning, contoured at 1 and represented in orthonormal axes with x parallel to a and z parallel to c*. (a) Twofold NCS rotation; (b) fourfold NCS rotation.

Figure 3.
Figure 3 Stereoscopic view projected along b showing a global superposition of the eight molecules present in the asymmetric unit of the monoclinic crystal form (red) with eight symmetry-related molecules of the tetragonal form (green). The a axis is horizontal and c* is vertical. The A chain is on the bottom left of the figure and the H chain on the top right. The figure was produced with O (Jones et al., 1991[Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119.]).

The above figures are reproduced from the cited reference with permission from the IUCr

Secondary reference #3

Title

Cloning and characterization of aoeb166, A novel mammalian antioxidant enzyme of the peroxiredoxin family.

Authors

B.Knoops, A.Clippe, C.Bogard, K.Arsalane, R.Wattiez, C.Hermans, E.Duconseille, P.Falmagne, A.Bernard.

Ref.

J Biol Chem, 1999, 274, 30451-30458. [DOI no: 10.1074/jbc.274.43.30451]

PubMed id

10521424

Figure 3.
Fig. 3. Analysis of AOEB166 gene expression in human tissues and cell lines. A, human multiple tissue Northern blot (CLONTECH) containing approximately 2 µg of poly(A^+) RNA of different tissue origins was analyzed for the presence of human AOEB166 mRNA. B, Northern blot containing 40 µg/lane of total RNA from human cell lines of different tissue origins was also hybridized with human AOEB166 cDNA probe. Cell lines were Caco-2 human colonic adenocarcinoma cell line, MRC-5 human fetal lung fibroblast cell line, ECV-304 human endothelial cell line, MDA-231 human breast cancer cell line, MCF-7 human breast cancer cell line, THP-1 human monocytic leukemia cell line, HT-29 human colonic adenocarcinoma cell line, LS174T human colonic adenocarcinoma cell line, T47D human breast cancer cell line, and HepG2 human hepatoblastoma cell line. Positions for 4.4 and 1.35 kilobases as marked by ribosomal markers are indicated. Both blots were stripped of the hAOEB166 probe and rehybridized with a human -actin probe to assess integrity and levels of RNA between lanes (small panels below each blot). C, quantitation of AOEB166 mRNA levels in human master dot blot (CLONTECH). The dot blot, containing poly(A^+) RNA normalized to the mRNA expression levels of eight different housekeeping genes, was hybridized with AOEB166 cDNA probe. mRNA levels were quantitated using phosphorimaging technology. Higher levels are detected in thyroid gland and at lower levels in pancreas. Yeast S. cerevisiae mRNA was used as negative control.

Figure 6.
Fig. 6. Peroxidase activity of recombinant hAOEB166. Time-dependent removal of H[2]O[2] (A) or TBHP ( B) by recombinant hAOEB166. The reaction mixture (200 µl) contained 50 mM Hepes-NaOH, pH 7.4, 2 mM DTT, 1 mM H[2]O[2] or 800 µM TBHP, and recombinant hAOEB166 (0.2 mg/ml). At the indicated times, the remaining concentration of H[2]O[2] or TBHP was measured in 20 µl of reaction mixture with ferrous ammonium sulfate/potassium thiocyanate and compared with standards. The reduction of H[2]O[2] or TBHP in absence of AOEB166 was also measured (none). Data are the means of duplicate experiments.

The above figures are reproduced from the cited reference with permission from the ASBMB