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PDBsum entry 1ucf

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RNA binding protein PDB id
1ucf
Jmol
Contents
Protein chain
188 a.a. *
Waters ×321
* Residue conservation analysis

References listed in PDB file
Key reference
Title The crystal structure of dj-1, A protein related to male fertility and parkinson'S disease.
Authors K.Honbou, N.N.Suzuki, M.Horiuchi, T.Niki, T.Taira, H.Ariga, F.Inagaki.
Ref. J Biol Chem, 2003, 278, 31380-31384. [DOI no: 10.1074/jbc.M305878200]
PubMed id 12796482
Abstract
DJ-1 is a multifunctional protein that plays essential roles in tissues with higher order biological functions such as the testis and brain. DJ-1 is related to male fertility, and its level in sperm decreases in response to exposure to sperm toxicants. DJ-1 has also been identified as a hydroperoxide-responsive protein. Recently, a mutation of DJ-1 was found to be responsible for familial Parkinson's disease. Here, we present the crystal structure of DJ-1 refined to 1.95-A resolution. DJ-1 forms a dimer in the crystal, and the monomer takes a flavodoxin-like Rossmann-fold. DJ-1 is structurally most similar to the monomer subunit of protease I, the intracellular cysteine protease from Pyrococcus horikoshii, and belongs to the Class I glutamine amidotransferase-like superfamily. However, DJ-1 contains an additional alpha-helix at the C-terminal region, which blocks the putative catalytic site of DJ-1 and appears to regulate the enzymatic activity. DJ-1 may induce conformational changes to acquire catalytic activity in response to oxidative stress.
Figure 3.
FIG. 3. Surface representations of the dimer interface and the opposite surface of DJ-1. The electrostatic surface potential of DJ-1 for the dimer interface (a) and the opposite surface (b) is shown. Red and blue represent negative and positive potentials, respectively. The surface model for the dimer interface (c) and the opposite surface of DJ-1 (d) in which the binding surface is encircled with a solid line are shown. The conserved and type conserved residues are shown in red and yellow, respectively. Compared with the opposite surface, the residues on the dimer interface are either conserved or type-conserved. Notably, the residues forming the putative catalytic site (encircled with a dotted line) are located close to the dimer interface and are highly conserved. Fig. 3 was prepared using GRASP (29).
Figure 4.
FIG. 4. Comparison of the monomer structures and the putative catalytic sites between DJ-1 and protease I. Ribbon diagrams of the monomer subunits of DJ-1 (a) and protease I (b). Secondary structure is color-coded as in Fig. 2a. c, the region around the putative active site of DJ-1 including 5, 5, and the nucleophile elbow in monomer A (in blue) and 8 and 9 in monomer B (in green). The residues Cys-106, His-126, and Val-128 in monomer A and Leu-166, Val-181, Lys-182, Pro-184 (a backbone oxygen), Val-186, and Leu-187 in monomer B are shown as ball-and-stick models. The His-126 imidazole ring forms hydrogen bonds with the main-chain carbonyl group of Pro-184 (monomer B) and the main-chain amide group of Val-128 (monomer A) are shown by the dotted lines. Thus, the His-126 imidazole ring does not take a preferable orientation for protease activity. Leu-166, mutated to proline in PARK7 patients, is shown in red. d, the region around the active site of protease I including the nucleophile elbow in which the catalytic residue Cys-100 is located. Protease I forms a hexamer, and the catalytic triad is formed in the dimer interface (monomer A is in blue, and monomer B is in green).
The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 31380-31384) copyright 2003.
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