1YD0

Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima bound to its catalytic divalent cation: manganese

Summary for 1YD0

• Entry DOI: 10.2210/pdb1yd0/pdb
• Related: 1D9X 1KFT 1LN0 1MK0 1YCZ 1YD1 1YD2 1YD3 1YD4 1YD5 1YD6
• Descriptor: UvrABC system protein C, MANGANESE (II) ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: dna binding protein
• Biological source: Thermotoga maritima
• Cellular location: Cytoplasm (By similarity): Q9WYA3
• Total number of polymer chains: 1
• Total formula weight: 11690.23

Authors

Truglio, J.J.,Rhau, B.,Croteau, D.L.,Wang, L.,Skorvaga, M.,Karakas, E.,DellaVecchia, M.J.,Wang, H.,Van Houten, B.,Kisker, C. (deposition date: 2004-12-23, release date: 2005-03-01, Last modification date: 2024-03-13)

Primary citation

Truglio, J.J.,Rhau, B.,Croteau, D.L.,Wang, L.,Skorvaga, M.,Karakas, E.,Dellavecchia, M.J.,Wang, H.,Van Houten, B.,Kisker, C.
Structural insights into the first incision reaction during nucleotide excision repair
Embo J., 24:885-894, 2005

PubMed Abstract: Nucleotide excision repair is a highly conserved DNA repair mechanism present in all kingdoms of life. The incision reaction is a critical step for damage removal and is accomplished by the UvrC protein in eubacteria. No structural information is so far available for the 3' incision reaction. Here we report the crystal structure of the N-terminal catalytic domain of UvrC at 1.5 A resolution, which catalyzes the 3' incision reaction and shares homology with the catalytic domain of the GIY-YIG family of intron-encoded homing endonucleases. The structure reveals a patch of highly conserved residues surrounding a catalytic magnesium-water cluster, suggesting that the metal binding site is an essential feature of UvrC and all GIY-YIG endonuclease domains. Structural and biochemical data strongly suggest that the N-terminal endonuclease domain of UvrC utilizes a novel one-metal mechanism to cleave the phosphodiester bond.

PubMed: 15692561
DOI: 10.1038/sj.emboj.7600568

Experimental method

X-RAY DIFFRACTION (1.5 Å)