PDBsum entry: 1yd5

DNA binding protein

PDB id: 1yd5

Contents

Protein chain

90 a.a. *

Metals

_MN ×3

Waters ×82

* Residue conservation analysis

PDB id:

1yd5

Name:

DNA binding protein

Title:

Crystal structure of the giy-yig n-terminal endonuclease dom uvrc from thermotoga maritima: point mutant n88a bound to i catalytic divalent cation

Structure:

Uvrabc system protein c. Chain: a. Fragment: n-terminal domain. Synonym: uvrc protein, excinuclease abc subunit c. Engineered: yes. Mutation: yes

Source:

Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.80Å R-factor: 0.182 R-free: 0.209

Authors:

J.J.Truglio,B.Rhau,D.L.Croteau,L.Wang,M.Skorvaga,E.Karakas, M.J.Dellavecchia,H.Wang,B.Van Houten,C.Kisker

Key ref:

J.J.Truglio et al. (2005). Structural insights into the first incision reaction during nucleotide excision repair. EMBO J, 24, 885-894. PubMed id: 15692561 DOI: 10.1038/sj.emboj.7600568

Date:

23-Dec-04 Release date: 01-Mar-05

Protein chain

Q9WYA3  (UVRC_THEMA) -  UvrABC system protein C

Seq: 557 a.a.

Struc: 90 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (1 term)
• Biological process: DNA repair (1 term)
• Biochemical function: nuclease activity (1 term)

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 (green cage). Residues in close proximity to the metal ion are shown in ball-and-stick representation.

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.