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89 a.a.
Key reference
DOI no: 10.1038/sj.emboj.7600568 EMBO J 24:885-894 (2005) PubMed id: 15692561
Structural insights into the first incision reaction during nucleotide excision repair. J.J.Truglio, B.Rhau, D.L.Croteau, L.Wang, M.Skorvaga, E.Karakas, M.J.Dellavecchia, H.Wang, B.Van Houten, C.Kisker. 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.
Selected figure(s)
Figure 4.
Figure 4 Stereo view of the active site of the 3' endonuclease domain. The metal ion is shown as a magenta sphere and the five surrounding water molecules as red spheres. Hydrogen bonds are shown as dotted lines. A simulated annealing omit map omitting the magnesium-water cluster, Glu 76, Arg 39 and Tyr 29 is shown at 1(blue, transparent) and an anomalous map is shown at 7
Figure 7.
Figure 7 Proposed reaction mechanism for 3' phosphodiester bond cleavage by UvrC. The metal ion fulfills the role of the Lewis acid and one of the water molecules coordinated to the metal acts as a general acid. Tyr 29 acts as the general base and hydrogen bonds to a metal-coordinated hydroxide. Due to this coordination scheme, Tyr 29 can accept a proton from a nucleophilic water molecule while simultaneously transferring its proton to the metal-bound hydroxide. Arg 39 and Lys 32 are responsible for stabilizing the negative charge of the free 5'-phosphate after DNA cleavage.The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2005, 24, 885-894) copyright 2005. Figures were selected by an automated process.
Literature references that cite this PDB file's key reference
PubMed id Reference
19651876 L.E.Corina, W.Qiu, A.Desai, and D.L.Herrin (2009).
Biochemical and mutagenic analysis of I-CreII reveals distinct but important roles for both the H-N-H and GIY-YIG motifs.Nucleic Acids Res, 37, 5810-5821.
18086711 G.Gasiunas, G.Sasnauskas, G.Tamulaitis, C.Urbanke, D.Razaniene, and V.Siksnys (2008).
Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family.Nucleic Acids Res, 36, 938-949. 19014591 K.H.Kaminska, M.Kawai, M.Boniecki, I.Kobayashi, and J.M.Bujnicki (2008).
Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site.BMC Struct Biol, 8, 48.
18539732 P.Lagerbäck, and K.Carlson (2008).
Amino acid residues in the GIY-YIG endonuclease II of phage T4 affecting sequence recognition and binding as well as catalysis.J Bacteriol, 190, 5533-5544.
18578568 S.C.Wolski, J.Kuper, P.Hänzelmann, J.J.Truglio, D.L.Croteau, B.Van Houten, and C.Kisker (2008).
Crystal structure of the FeS cluster-containing nucleotide excision repair helicase XPD.PLoS Biol, 6, e149.
PDB code: 2vsf
17245438 E.Karakas, J.J.Truglio, D.Croteau, B.Rhau, L.Wang, B.Van Houten, and C.Kisker (2007).
Structure of the C-terminal half of UvrC reveals an RNase H endonuclease domain with an Argonaute-like catalytic triad.EMBO J, 26, 613-622.
PDB codes: 2nrr 2nrt 2nrv 2nrw 2nrx 2nrz
17626614 E.M.Ibryashkina, M.V.Zakharova, V.B.Baskunov, E.S.Bogdanova, M.O.Nagornykh, M.M.Den'mukhamedov, B.S.Melnik, A.Kolinski, D.Gront, M.Feder, A.S.Solonin, and J.M.Bujnicki (2007).
Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily.BMC Struct Biol, 7, 48.
16582101 Q.Liu, V.Derbyshire, M.Belfort, and D.R.Edgell (2006).
Distance determination by GIY-YIG intron endonucleases: discrimination between repression and cleavage functions.Nucleic Acids Res, 34, 1755-1764.
16646971 S.Dunin-Horkawicz, M.Feder, and J.M.Bujnicki (2006).
Phylogenomic analysis of the GIY-YIG nuclease superfamily.BMC Genomics, 7, 98. The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.
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