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Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8

¹ RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230-0045, Japan
² RIKEN Harima Institute at SPring-8, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan
³ Protein Design Laboratory, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
⁴ Structure and Function of Biomolecules, PRESTO, Japan Science and Technology Corporation, Kawaguchi, Saitama 332-0012, Japan
⁵ Global Scientific Information and Computing Center, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
⁶ Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
⁷ Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
⁸ Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
⁹ Structural Bioinformatics Laboratory, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan

Reprint requests to: Shigeyuki Yokoyama, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan; e-mail: yokoyama{at}biochem.s.u-tokyo.ac.jp; fax: 81-45-503-9195.

The TT1542 protein from Thermus thermophilus HB8 is annotated as a conserved hypothetical protein, and belongs to the DUF158 family in the Pfam database. A BLAST search revealed that homologs of TT1542 are present in a wide range of organisms. The TT1542 homologs in eukaryotes, PIG-L in mammals, and GPI12 in yeast and protozoa, have N-acetylglucosaminylphosphatidylinositol (GlcNAc-PI) de-N-acetylase activity. Although most of the homologs in prokaryotes are hypothetical and have no known function, Rv1082 and Rv1170 from Mycobacterium tuberculosis are enzymes involved in the mycothiol detoxification pathway. Here we report the crystal structure of the TT1542 protein at 2.0 Å resolution, which represents the first structure for this superfamily of proteins. The structure of the TT1542 monomer consists of a twisted ß-sheet composed of six parallel ß-strands and one antiparallel ß-strand (with the strand order 3-2-1-4-5-7-6) sandwiched between six -helices. The N-terminal five ß-strands and four -helices form an incomplete Rossmann fold-like structure. The structure shares some similarity to the sugar-processing enzymes with Rossmann fold-like domains, especially those of the GPGTF (glycogen phosphorylase/glycosyl transferase) superfamily, and also to the NAD(P)-binding Rossmann fold domains. TT1542 is a homohexamer in the crystal and in solution, the six monomers forming a cylindrical structure. Putative active sites are suggested by the structure and conserved amino acid residues.

Keywords: Thermus thermophilus HB8; conserved protein TT1542; GlcNAc-PI de-N-acetylase homolog; GlcNAc-Ins de-N-acetylase homolog; mycothiol S-conjugate amidase homolog; DUF158; crystallography

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