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Solution structure of the ubiquitin-like domain of human DC-UbP from dendritic cells

¹ Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, People’s Republic of China
² Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Shanghai 201203, People’s Republic of China
³ Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
⁴ Institute of Immunology, Secondary Military Medical University, Shanghai 200433, People’s Republic of China

(RECEIVED March 11, 2005; FINAL REVISION April 26, 2005; ACCEPTED April 28, 2005)

The previously identified dendritic cell-derived ubiquitin-like protein (DC-UbP) was implicated in cellular differentiation and apoptosis. Sequence alignment suggested that it contains a ubiquitin-like (UbL) domain in the C terminus. Here, we present the solution NMR structure and backbone dynamics of the UbL domain of DC-UbP. The overall structure of the domain is very similar to that of Ub despite low similarity (<30%) in amino-acid sequence. One distinct feature of the domain structure is its highly positively charged surface that is different from the corresponding surfaces of the well-known UbL modifiers, Ub, NEDD8, and SUMO-1. The key amino-acid residues responsible for guiding polyubiquitinated proteins to proteasome degradation in Ub are not conserved in the UbL domain. This implies that the UbL domain of DC-UbP may have its own specific interaction partners with other yet unknown cellular functions related to the Ub pathway.

Keywords: solution structure; dynamics; ubiquitin-like domain; DC-UbP; NMR

Abbreviations: CSI, chemical shift index • DC-UbP, dendritic cell-derived ubiquitin-like protein • HSQC, heteronuclear single quantum coherence • IPTG, isopropyl-,D-thiogalactopyranoside • NOESY, nuclear Overhauser effect spectroscopy • ORF, open reading frame • ppm, parts per million • RMSD, root-mean-square deviation • SA, simulated annealing • Ub, ubiquitin • UbL, ubiquitin-like • UBLs, ubiquitin-like modifiers • UDP, ubiquitin-domain protein • VdW, van der Waals

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051455505.

Reprint requests to: Hong-Yu Hu, Institute of Biochemistry and Cell Biology, 320 Yue-yang Road, Shanghai 200031, PRC; e-mail: hyhu{at}sibs.ac.cn; fax: +86-021-54921011; or Dong-Hai Lin, Shanghai Institute of Materia Medica, 555 Zuchongzhi Road, Shanghai 201203, PRC; e-mail: dhlin{at}mail.shcnc.ac.cn; fax: +86-021-50806036.

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