2D07

Crystal Structure of SUMO-3-modified Thymine-DNA Glycosylase

Summary for 2D07

• Entry DOI: 10.2210/pdb2d07/pdb
• Descriptor: G/T mismatch-specific thymine DNA glycosylase, Ubiquitin-like protein SMT3B (3 entities in total)
• Functional Keywords: hydrolase
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: Q13569 P61956
• Total number of polymer chains: 2
• Total formula weight: 36800.96

Authors

Baba, D.,Maita, N.,Jee, J.G.,Uchimura, Y.,Saitoh, H.,Sugasawa, K.,Hanaoka, F.,Tochio, H.,Hiroaki, H.,Shirakawa, M. (deposition date: 2005-07-26, release date: 2006-06-06, Last modification date: 2023-10-25)

Primary citation

Baba, D.,Maita, N.,Jee, J.G.,Uchimura, Y.,Saitoh, H.,Sugasawa, K.,Hanaoka, F.,Tochio, H.,Hiroaki, H.,Shirakawa, M.
Crystal Structure of SUMO-3-modified Thymine-DNA Glycosylase
J.Mol.Biol., 359:137-147, 2006

PubMed Abstract: Modification of cellular proteins by the small ubiquitin-like modifier SUMO is important in regulating various cellular events. Many different nuclear proteins are targeted by SUMO, and the functional consequences of this modification are diverse. For most proteins, however, the functional and structural consequences of modification by specific SUMO isomers are unclear. Conjugation of SUMO to thymine-DNA glycosylase (TDG) induces the dissociation of TDG from its product DNA. Structure determination of the TDG central region conjugated to SUMO-1 previously suggested a mechanism in which the SUMOylation-induced conformational change in the C-terminal region of TDG releases TDG from tight binding to its product DNA. Here, we have determined the crystal structure of the central region of TDG conjugated to SUMO-3. The overall structure of SUMO-3-conjugated TDG is similar to the previously reported structure of TDG conjugated to SUMO-1, despite the relatively low level of amino acid sequence similarity between SUMO-3 and SUMO-1. The two structures revealed that the sequence of TDG that resembles the SUMO-binding motif (SBM) can form an intermolecular beta-sheet with either SUMO-1 or SUMO-3. Structural comparison with the canonical SBM shows that this SBM-like sequence of TDG retains all of the characteristic interactions of the SBM, indicating sequence diversity in the SBM.

PubMed: 16626738
DOI: 10.1016/j.jmb.2006.03.036

Experimental method

X-RAY DIFFRACTION (2.1 Å)