PDBsum entry 2d1h

Transcription

PDB id

2d1h

Contents

			Protein chains

					102 a.a.

			Waters ×90

References listed in PDB file

Key reference

Title

The putative DNA-Binding protein sto12a from the thermoacidophilic archaeon sulfolobus tokodaii contains intrachain and interchain disulfide bonds.

Authors

A.Shinkai, S.Sekine, A.Urushibata, T.Terada, M.Shirouzu, S.Yokoyama.

Ref.

J Mol Biol, 2007, 372, 1293-1304. [DOI no: 10.1016/j.jmb.2007.07.051]

PubMed id

17720190

Abstract

The Sto12a protein, from the thermoacidophilic archaeon Sulfolobus tokodaii, has been identified as a small putative DNA-binding protein. Most of the proteins with a high level of amino acid sequence homology to this protein are derived from members of the Sulfolobaceae family, including a transcriptional regulator. We determined the crystal structure of Sto12a at 2.05 A resolution by multiple-wavelength anomalous dispersion phasing from the selenomethionine-containing protein crystal. This is the first structure of a member of this family of DNA-binding proteins. The Sto12a protein forms a homodimer, and the structure is composed of an N-terminal alpha-helix, a winged-helix-turn-helix domain, and a C-terminal alpha-helix that forms an interchain antiparallel coiled coil. The two winged-helix domains are located at both ends of the coiled coil, with putative DNA-recognition helices separated by approximately 34 A. A structural homology search indicated that the winged-helix domain shared a high level of homology with those found in B-DNA- or Z-DNA-binding proteins from various species, including archaea, bacteria, and human, despite a low level of sequence similarity. The unique structural features of the Sto12a protein include intrachain and interchain disulfide bonds, which stabilize the chain and homodimer structures. There are three cysteine residues: Cys15 and Cys16 in the N-terminal alpha-helix, and Cys100 in the C-terminal alpha-helix. Cys15 is involved in an interchain disulfide bridge with the other Cys15, and Cys16 forms an intrachain disulfide bridge with Cys100. This is a novel fold among winged-helix DNA-binding proteins. Possible DNA-binding interactions of the Sto12a protein are discussed based on the crystal structure of Sto12a and comparisons to other winged-helix DNA-binding proteins.



	Figure 3. Fig. 3. Overall structure of Sto12a. (a) Stereoview of the Sto12a dimer. α-Helices and β-strands are presented in red and blue, respectively. The side chains of Cys15, Cys16, and Cys100 are depicted by stick models, and residues and disulfide bridges are presented in green. The side chains of Asp11 and Lys18 are shown by stick models, and the residues are presented in yellow, with the side-chain O atom of Asp11 and the side-chain N atom of Lys18 presented in red and blue, respectively. The H0–H4 helices and the S1–S3 strands on chain A are indicated. (b) An end view of the dimer, viewed down the H4 helical axis of chain A from the N terminus. The colors of chain A are the same as in (a). Chain B is presented in gray. The H4 helices of chains A and B are indicated as H4 and H4′, respectively. Residues Glu72–Arg78 of chain A, and residues Met2–Glu4 and Glu72–Arg78 of chain B are disordered and are missing from the figure. The first and last residues in the gap are indicated. These figures were prepared with PyMol [http://www.pymol.org].		Figure 6. Fig. 6. Models of the Sto12a dimer complexed with DNA are shown in a ribbon representation. The two Sto12a monomers are presented in magenta and blue, and cysteine residues are depicted as ball-and-stick models. DNA molecules were taken from the coordinates of the Genesis/DNA complex (a and b) and the RFX1/DNA complex (c and d) and are presented in yellow and green. Amino acid residues 72–78, which are missing from the coordinates, were modeled and are shown as transparent tubes at the tip of the β-hairpin of the winged helix. (b and d) The same as in (a) and (c), respectively, but viewed from the orientation rotated around the long axis by 90°. These figures were prepared with PyMol [http://www.pymol.org].

PROCHECK

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