PDBsum entry 2nrt

Hydrolase

PDB id: 2nrt

Contents

Protein chain

217 a.a. *

Metals

_CL ×5

Waters ×206

* Residue conservation analysis

PDB id:

2nrt

Name:

Hydrolase

Title:

Crystal structure of thE C-terminal half of uvrc

Structure:

Uvrabc system protein c. Chain: a. Fragment: rnase h endonuclease and helix hairpin helix domains (residues 339-557). Synonym: protein uvrc, excinuclease abc subunit c. Engineered: yes

Source:

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

Resolution:

1.50Å R-factor: 0.187 R-free: 0.221

Authors:

E.Karakas,J.J.Truglio,C.Kisker

Key ref:

E.Karakas et al. (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. PubMed id: 17245438 DOI: 10.1038/sj.emboj.7601497

Date:

02-Nov-06 Release date: 06-Feb-07

Protein chain

Q9WYA3  (UVRC_THEMA) -  UvrABC system protein C from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 557 a.a.

Struc: 217 a.a.

DOI no: 10.1038/sj.emboj.7601497

EMBO J 26:613-622 (2007)

PubMed id: 17245438

Structure of the C-terminal half of UvrC reveals an RNase H endonuclease domain with an Argonaute-like catalytic triad.

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

ABSTRACT

Removal and repair of DNA damage by the nucleotide excision repair pathway requires two sequential incision reactions, which are achieved by the endonuclease UvrC in eubacteria. Here, we describe the crystal structure of the C-terminal half of UvrC, which contains the catalytic domain responsible for 5' incision and a helix-hairpin-helix-domain that is implicated in DNA binding. Surprisingly, the 5' catalytic domain shares structural homology with RNase H despite the lack of sequence homology and contains an uncommon DDH triad. The structure also reveals two highly conserved patches on the surface of the protein, which are not related to the active site. Mutations of residues in one of these patches led to the inability of the enzyme to bind DNA and severely compromised both incision reactions. Based on our results, we suggest a model of how UvrC forms a productive protein-DNA complex to excise the damage from DNA.

Selected figure(s)

Figure 4.
Figure 4 Electrostatic surface potential and sequence conservation of the C-terminal half of UvrC. (A) Electrostatic surface potential was calculated with PyMol/APBS and contoured at 10 k[B]T. The top panel features the active site of the protein and the bottom view is a 180° rotation. (B) Sequence conservation using the same orientations as in (A). The degree of conservation was obtained by alignment of 47 UvrC sequences with ClustalX. Strictly conserved (red), very highly conserved (blue), highly conserved (green) and moderately conserved (black) amino acids are highlighted. The remainder of the protein is colored in gray. Bound sulfate molecules are shown in all-bonds representation. Selected amino acids are labeled.

Figure 6.
Figure 6 DNA binding model. (A) Side-by-side comparison of the (HhH)[2] domain of RuvA (left), TmUvrC (center) and EcUvrC (right) after superposition. The DNA backbone of the RuvA/DNA complex (left panel) is shown as an orange worm. Selected residues are shown in all-bonds representation and are labeled. The N- and C-termini are indicated. The HhHI and HhHII motifs are colored yellow and green, respectively. The helical linker between the two motifs is colored blue. (B) The endonuclease domains of eight TmUvrC^C-term structures are superimposed to show the orientation of the (HhH)[2] domains relative to the endonuclease domain in the different crystal forms. (C) Model of TmUvrC interacting with DNA based on a superposition with the Tn5 transposase–DNA complex. The endonuclease and (HhH)[2] domain of TmUvrC are colored yellow and cyan, respectively. The DNA is orange and drawn with spokes for clarity. The side chains of the catalytic triad and D405 are depicted as all-bonds. The bound magnesium is shown as a green sphere. In the left panel, the (HhH)[2] domain is depicted in the position found in the crystal structure. The DNA-interacting region of the (HhH)[2] domain is shown in red. In the right panel, the (HhH)[2] domain has been rotated to form a productive UvrC/DNA complex. A dashed line indicates the connection point between the endonuclease domain and the (HhH)[2] domain.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2007, 26, 613-622) copyright 2007.

Figures were selected by the author.