PDBsum entry: 2o4g

Hydrolase

PDB id: 2o4g

Contents

Protein chains

217 a.a. *

Ligands

TMP ×4

Metals

_MG ×8

Waters ×190

* Residue conservation analysis

PDB id:

2o4g

Name:

Hydrolase

Title:

Structure of trex1 in complex with a nucleotide

Structure:

Three prime repair exonuclease 1. Chain: a, b, c, d. Fragment: trex1 exonuclease. Synonym: 3'-5' exonuclease trex1. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: trex1. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

2.35Å R-factor: 0.206 R-free: 0.255

Authors:

M.Brucet,M.J.Macias,I.Fita,A.Celada

Key ref:

M.Brucet et al. (2007). Structure of the dimeric exonuclease TREX1 in complex with DNA displays a proline-rich binding site for WW Domains. J Biol Chem, 282, 14547-14557. PubMed id: 17355961 DOI: 10.1074/jbc.M700236200

Date:

04-Dec-06 Release date: 13-Mar-07

Protein chains

Q91XB0  (TREX1_MOUSE) -  Three prime repair exonuclease 1

Seq: 314 a.a.

Struc: 217 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.11.2 - Exodeoxyribonuclease Iii.
• Reaction: Degradation of double-stranded DNA. It acts progressively in a 3'- to 5'-direction, releasing nucleoside 5'-phosphates.

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (1 term)
• Biochemical function: nucleic acid binding (2 terms)

DOI no: 10.1074/jbc.M700236200

J Biol Chem 282:14547-14557 (2007)

PubMed id: 17355961

Structure of the dimeric exonuclease TREX1 in complex with DNA displays a proline-rich binding site for WW Domains.

M.Brucet, J.Querol-Audí, M.Serra, X.Ramirez-Espain, K.Bertlik, L.Ruiz, J.Lloberas, M.J.Macias, I.Fita, A.Celada.

ABSTRACT

TREX1 is the most abundant mammalian 3' --> 5' DNA exonuclease. It has been described to form part of the SET complex and is responsible for the Aicardi-Goutières syndrome in humans. Here we show that the exonuclease activity is correlated to the binding preferences toward certain DNA sequences. In particular, we have found three motifs that are selected, GAG, ACA, and CTGC. To elucidate how the discrimination occurs, we determined the crystal structures of two murine TREX1 complexes, with a nucleotide product of the exonuclease reaction, and with a single-stranded DNA substrate. Using confocal microscopy, we observed TREX1 both in nuclear and cytoplasmic subcellular compartments. Remarkably, the presence of TREX1 in the nucleus requires the loss of a C-terminal segment, which we named leucine-rich repeat 3. Furthermore, we detected the presence of a conserved proline-rich region on the surface of TREX1. This observation points to interactions with proline-binding domains. The potential interacting motif "PPPVPRPP" does not contain aromatic residues and thus resembles other sequences that select SH3 and/or Group 2 WW domains. By means of nuclear magnetic resonance titration experiments, we show that, indeed, a polyproline peptide derived from the murine TREX1 sequence interacted with the WW2 domain of the elongation transcription factor CA150. Co-immunoprecipitation studies confirmed this interaction with the full-length TREX1 protein, thereby suggesting that TREX1 participates in more functional complexes than previously thought.

Selected figure(s)

Figure 4.
FIGURE 4. Structure of TREX1 in complex with DNA. A, extra electron density observed in the active center, indicating the presence of a 4-mer single-stranded DNA (orange atom-type sticks). The potential surface representation shows the predominantly negatively charged catalytic center and the region adjacent to the disordered loop 167-174. B, structure of the active site in complex with the single-stranded DNA. Residues responsible for interaction with DNA are depicted in yellow atom-type sticks. Arg^174, only well structured in monomer B, and the catalytic residue His^195 mutated to Ala are also shown. C, TREX1 electrostatic potential surface showing the relative position of the DNA in complex with the dimer. The dimer possesses little positive charge except in the regions adjacent to the active sites. The cleft that connects the two active sites presents an overall negative charge. D, structural superimposition of the active site of TREX1 in the presence of a DNA substrate (cyan) and in the presence of a dTMP nucleotide (green), product of the exonuclease reaction.

Figure 5.
FIGURE 5. DNA interaction with TREX1 and Klenow and nucleotide interaction with TREX1. A, ribbon diagram superimposition of TREX1 (cyan) and the exonuclease Klenow fragment (purple) in complex with single-stranded DNA (4-mer in TREX1, 3-mer in Klenow, PDB 1KSP), showing that the cores and most secondary structural elements are conserved. B, model showing the putative interaction of TREX1 with a double-stranded DNA (red and orange). The model was constructed by a superposition of the structure of the Klenow fragment bound to double-stranded DNA (PDB 1KLN). The regions predicted to be responsible for DNA binding are indicated (Trp^188 in yellow, disordered loop in black, and polyproline loop in green).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 14547-14557) copyright 2007.

Figures were selected by an automated process.