PDBsum entry 1gcc

Transcription/DNA

PDB id

1gcc

Contents

			Protein chain

					63 a.a. *

			DNA/RNA

* Residue conservation analysis

References listed in PDB file

Key reference

Title

A novel mode of DNA recognition by a beta-Sheet revealed by the solution structure of the gcc-Box binding domain in complex with DNA.

Authors

M.D.Allen, K.Yamasaki, M.Ohme-Takagi, M.Tateno, M.Suzuki.

Ref.

Embo J, 1998, 17, 5484-5496. [DOI no: 10.1093/emboj/17.18.5484]

PubMed id

9736626

Abstract

The 3D solution structure of the GCC-box binding domain of a protein from Arabidopsis thaliana in complex with its target DNA fragment has been determined by heteronuclear multidimensional NMR in combination with simulated annealing and restrained molecular dynamic calculation. The domain consists of a three-stranded anti-parallel beta-sheet and an alpha-helix packed approximately parallel to the beta-sheet. Arginine and tryptophan residues in the beta-sheet are identified to contact eight of the nine consecutive base pairs in the major groove, and at the same time bind to the sugar phosphate backbones. The target DNA bends slightly at the central CG step, thereby allowing the DNA to follow the curvature of the beta-sheet.



	Figure 2. Figure 2 Comparison of GBD with a zinc finger. (A) Superposition of the backbones of 46 GBD structures, Lys145-Val206, in the absence of the DNA refined by simulated annealing. Different colors are used for indicating the secondary structural elements. The N- and C-termini are labeled. (B) A diagrammatic drawing of the final structure made by energy minimization of the mean co-ordinates of the ensemble shown in (A), superimposed on a presentation of electropolarization. Positive charges are shown in blue and negative charges in red. The side that recognizes DNA is indicated with an arrow. (C) The 3D structure and electropolarization of the first zinc finger of SWI5 (Protein Data Bank code 1NCS) shown in the same way as in (B).		Figure 5. Figure 5 Contacts between GBD and the GCC-box. (A) A stereo subfigure of part of the GBD -DNA complex structure. The contacts are indicated by broken lines with different colors; green for hydrogen bonds and yellow for ionic contacts. Different colors are used for the coding (crimson) and complementary (cyan) strands. (B) A diagrammatic representation of the contacts identified after restrained molecular dynamic calculation. The DNA is drawn by looking into the major groove. Yellow circles represent the phosphate groups. The contacted bases are highlighted in cyan. The same color code as in (A) is used for typing the contacts and, in addition, brown for hydrophobic contacts. The distance between Glu160 and C19 is slightly larger than the standard hydrogen bonding distance (shown by a broken line). The up -down transcription direction is indicated. The coding and complementary strands are labeled. Gd: guanidyl group. (C) A diagrammatic representation of the NOEs observed between amino acid residues and the target DNA. The bases with which the NOEs are observed are highlighted in orange. (D) The three stranded -sheet of GBD. Residues are colored differently depending on the function; base-contacting only (blue), backbone-binding only (yellow) and having both functions (green). An ellipsoid is drawn by connecting the green positions, which is divided into two halves by the broken line that crosses Ala159. The CG step is highlighted in cyan. The up -down transcription direction is indicated. The coding and complementary strands are labeled. (E) A two stranded -sheet of the MetJ -Arc type. The figure was made using the co-ordinates of the MetJ -DNA complex (Protein Data Base code 1CMA). The six amino acid positions used for base recognition by the MetJ -Arc family are in blue. An ellipsoid is drawn enclosing the blue residues. Compare the ellipsoid with the larger ellipsoid shown in (D) for an appreciation of the difference in size of the two interaction sites.

PROCHECK

	Headers