2D1H

Crystal structure of ST1889 protein from thermoacidophilic archaeon Sulfolobus tokodaii

Summary for 2D1H

• Entry DOI: 10.2210/pdb2d1h/pdb
• Descriptor: 109aa long hypothetical transcriptional regulator (2 entities in total)
• Functional Keywords: helix-turn-helix, intermolecular and intramolecular s-s bonds, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, transcription
• Biological source: Sulfolobus tokodaii
• Total number of polymer chains: 2
• Total formula weight: 25478.96

Authors

Shinkai, A.,Sekine, S.,Terada, T.,Shirouzu, M.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2005-08-22, release date: 2006-09-05, Last modification date: 2024-10-23)

Primary citation

Shinkai, A.,Sekine, S.,Urushibata, A.,Terada, T.,Shirouzu, M.,Yokoyama, S.
The putative DNA-binding protein Sto12a from the thermoacidophilic archaeon Sulfolobus tokodaii contains intrachain and interchain disulfide bonds.
J.Mol.Biol., 372:1293-1304, 2007

PubMed 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.

PubMed: 17720190
DOI: 10.1016/j.jmb.2007.07.051

Experimental method

X-RAY DIFFRACTION (2.05 Å)