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DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein.

Duan MR, Nan J, Liang YH, Mao P, Lu L, Li L, Wei C, Lai L, Li Y, Su XD - Nucleic Acids Res. (2007)

Bottom Line: Previous investigations showed that DNA binding of the WRKY proteins was localized at the WRKY domains and these domains may define novel zinc-binding motifs.A novel zinc-binding site is situated at one end of the beta-sheet, between strands beta4 and beta5.These results provided us with structural information to understand the mechanism of transcriptional control and signal transduction events of the WRKY proteins.

View Article: PubMed Central - PubMed

Affiliation: The National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing 100871, PR China.

ABSTRACT
WRKY proteins, defined by the conserved WRKYGQK sequence, are comprised of a large superfamily of transcription factors identified specifically from the plant kingdom. This superfamily plays important roles in plant disease resistance, abiotic stress, senescence as well as in some developmental processes. In this study, the Arabidopsis WRKY1 was shown to be involved in the salicylic acid signaling pathway and partially dependent on NPR1; a C-terminal domain of WRKY1, AtWRKY1-C, was constructed for structural studies. Previous investigations showed that DNA binding of the WRKY proteins was localized at the WRKY domains and these domains may define novel zinc-binding motifs. The crystal structure of the AtWRKY1-C determined at 1.6 A resolution has revealed that this domain is composed of a globular structure with five beta strands, forming an antiparallel beta-sheet. A novel zinc-binding site is situated at one end of the beta-sheet, between strands beta4 and beta5. Based on this high-resolution crystal structure and site-directed mutagenesis, we have defined and confirmed that the DNA-binding residues of AtWRKY1-C are located at beta2 and beta3 strands. These results provided us with structural information to understand the mechanism of transcriptional control and signal transduction events of the WRKY proteins.

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Related in: MedlinePlus

The zinc coordination environment. (A) 3Fo-2Fc electron-density map. The coordination of the zinc ion by Cys332, Cys337, His361 and His363 was shown. The map was prepared using CCP4 program suite and displayed with Pymol at the contour of 1.5σ level. The zinc ion is shown as a purple sphere and the zinc-coordinating residues are represented by stick (yellow for C, red for O, blue for N, orange for S, respectively). (B) The distances between the zinc ion and the coordinate residues. The orientation and colors are the same as shown in Figure 4A.
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Figure 4: The zinc coordination environment. (A) 3Fo-2Fc electron-density map. The coordination of the zinc ion by Cys332, Cys337, His361 and His363 was shown. The map was prepared using CCP4 program suite and displayed with Pymol at the contour of 1.5σ level. The zinc ion is shown as a purple sphere and the zinc-coordinating residues are represented by stick (yellow for C, red for O, blue for N, orange for S, respectively). (B) The distances between the zinc ion and the coordinate residues. The orientation and colors are the same as shown in Figure 4A.

Mentions: One of the important features resolved by the high-resolution crystal structure of AtWRKY1-C is the well-ordered zinc-binding site. As shown in the electron density map in Figure 4A, the high-resolution data of 1.6 Å made it possible to distinguish the zinc coordination with all the ligand atoms, and it was clearly shown that the Nδ of His361 and the Nε of His363, coordinate to the zinc ion (Figure 4A and B). The distances between the ligand atoms and the zinc ion are 2.06 Å (Zn–Nδ of His361), 2.07 Å (Zn–Nε of His363), 2.28 Å (Zn–Sγ of Cys332), 2.27 Å (Zn–Sγ of Cys337), all the distances are well within the ideal distances of a zinc-binding site in proteins (49).Figure 4.


DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein.

Duan MR, Nan J, Liang YH, Mao P, Lu L, Li L, Wei C, Lai L, Li Y, Su XD - Nucleic Acids Res. (2007)

The zinc coordination environment. (A) 3Fo-2Fc electron-density map. The coordination of the zinc ion by Cys332, Cys337, His361 and His363 was shown. The map was prepared using CCP4 program suite and displayed with Pymol at the contour of 1.5σ level. The zinc ion is shown as a purple sphere and the zinc-coordinating residues are represented by stick (yellow for C, red for O, blue for N, orange for S, respectively). (B) The distances between the zinc ion and the coordinate residues. The orientation and colors are the same as shown in Figure 4A.
© Copyright Policy - openaccess
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1851648&req=5

Figure 4: The zinc coordination environment. (A) 3Fo-2Fc electron-density map. The coordination of the zinc ion by Cys332, Cys337, His361 and His363 was shown. The map was prepared using CCP4 program suite and displayed with Pymol at the contour of 1.5σ level. The zinc ion is shown as a purple sphere and the zinc-coordinating residues are represented by stick (yellow for C, red for O, blue for N, orange for S, respectively). (B) The distances between the zinc ion and the coordinate residues. The orientation and colors are the same as shown in Figure 4A.
Mentions: One of the important features resolved by the high-resolution crystal structure of AtWRKY1-C is the well-ordered zinc-binding site. As shown in the electron density map in Figure 4A, the high-resolution data of 1.6 Å made it possible to distinguish the zinc coordination with all the ligand atoms, and it was clearly shown that the Nδ of His361 and the Nε of His363, coordinate to the zinc ion (Figure 4A and B). The distances between the ligand atoms and the zinc ion are 2.06 Å (Zn–Nδ of His361), 2.07 Å (Zn–Nε of His363), 2.28 Å (Zn–Sγ of Cys332), 2.27 Å (Zn–Sγ of Cys337), all the distances are well within the ideal distances of a zinc-binding site in proteins (49).Figure 4.

Bottom Line: Previous investigations showed that DNA binding of the WRKY proteins was localized at the WRKY domains and these domains may define novel zinc-binding motifs.A novel zinc-binding site is situated at one end of the beta-sheet, between strands beta4 and beta5.These results provided us with structural information to understand the mechanism of transcriptional control and signal transduction events of the WRKY proteins.

View Article: PubMed Central - PubMed

Affiliation: The National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing 100871, PR China.

ABSTRACT
WRKY proteins, defined by the conserved WRKYGQK sequence, are comprised of a large superfamily of transcription factors identified specifically from the plant kingdom. This superfamily plays important roles in plant disease resistance, abiotic stress, senescence as well as in some developmental processes. In this study, the Arabidopsis WRKY1 was shown to be involved in the salicylic acid signaling pathway and partially dependent on NPR1; a C-terminal domain of WRKY1, AtWRKY1-C, was constructed for structural studies. Previous investigations showed that DNA binding of the WRKY proteins was localized at the WRKY domains and these domains may define novel zinc-binding motifs. The crystal structure of the AtWRKY1-C determined at 1.6 A resolution has revealed that this domain is composed of a globular structure with five beta strands, forming an antiparallel beta-sheet. A novel zinc-binding site is situated at one end of the beta-sheet, between strands beta4 and beta5. Based on this high-resolution crystal structure and site-directed mutagenesis, we have defined and confirmed that the DNA-binding residues of AtWRKY1-C are located at beta2 and beta3 strands. These results provided us with structural information to understand the mechanism of transcriptional control and signal transduction events of the WRKY proteins.

Show MeSH
Related in: MedlinePlus