PDBsum entry: 3b6p

Hydrolase

PDB id: 3b6p

Contents

Protein chains

217 a.a. *

Ligands

TMP ×4

Metals

_NA ×4

_ZN ×4

Waters ×471

* Residue conservation analysis

PDB id:

3b6p

Name:

Hydrolase

Title:

Structure of trex1 in complex with a nucleotide and inhibitor ions (sodium and zinc)

Structure:

Three prime repair exonuclease 1. Chain: a, b, c, d. Fragment: trex1 exonuclease, unp residues 9-245. Synonym: 3'-5' exonuclease trex1. Engineered: yes

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: trex1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.30Å R-factor: 0.248 R-free: 0.285

Authors:

M.Brucet,J.Querol-Audi,I.Fita,A.Celada

Key ref:

M.Brucet et al. (2008). Structural and biochemical studies of TREX1 inhibition by metals. Identification of a new active histidine conserved in DEDDh exonucleases. Protein Sci, 17, 2059-2069. PubMed id: 18780819 DOI: 10.1110/ps.036426.108

Date:

29-Oct-07 Release date: 23-Sep-08

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: 10.1110/ps.036426.108

Protein Sci 17:2059-2069 (2008)

PubMed id: 18780819

Structural and biochemical studies of TREX1 inhibition by metals. Identification of a new active histidine conserved in DEDDh exonucleases.

M.Brucet, J.Querol-Audí, K.Bertlik, J.Lloberas, I.Fita, A.Celada.

ABSTRACT

TREX1 is the major exonuclease in mammalian cells, exhibiting the highest level of activity with a 3'-->5' activity. This exonuclease is responsible in humans for Aicardi-Goutières syndrome and for an autosomal dominant retinal vasculopathy with cerebral leukodystrophy. In addition, this enzyme is associated with systemic lupus erythematosus. TREX1 belongs to the exonuclease DEDDh family, whose members display low levels of sequence identity, while possessing a common fold and active site organization. For these exonucleases, a catalytic mechanism has been proposed that involves two divalent metal ions bound to the DEDD motif. Here we studied the interaction of TREX1 with the monovalent cations lithium and sodium. We demonstrate that these metals inhibit the exonucleolytic activity of TREX1, as measured by the classical gel method, as well as by a new technique developed for monitoring the real-time exonuclease reaction. The X-ray structures of the enzyme in complex with these two cations and with a nucleotide, a product of the exonuclease reaction, were determined at 2.1 A and 2.3 A, respectively. A comparison with the structures of the active complexes (in the presence of magnesium or manganese) explains that the inhibition mechanism is caused by the noncatalytic metals competing with distinct affinities for the two metal-binding sites and inducing subtle rearrangements in active centers. Our analysis also reveals that a histidine residue (His124), highly conserved in the DEDDh family, is involved in the activity of TREX1, as confirmed by mutational studies. Our results shed further light on the mechanism of activity of the DEDEh family of exonucleases.

Selected figure(s)

Figure 2.
TREX1 --dTMP --ion complexes. (A) Overall structure of the sodium complex, representative of the organization of the three complexes (magnesium, lithium, and sodium). (B --D) Stereoviews of the metal-binding sites of the TREX1 complexes with dTMP and metal ions (B) magnesium, (C) lithium, and (D) sodium. The overall conformation of the molecular dimer of TREX1 is shown with ribbons (in gray), while dTMP molecules are represented with sticks and metal cations as spheres in green for magnesium (B), blue for lithium (C), orange and magenta for sodium and a heavier undetermined metal (X), respectively (D). The amino and carboxy ends are labeled as N and C, while the two metal-binding sites are indicated as A and B. Stereoviews of the catalytic residues from the DEDDh motif with dTMP and solvent molecules (red spheres) in the vicinity are also shown. The difference (Fo-Fc) maps at 2.5 [sigma] are shown for the lithium and sodium structures. Coordination bonds of the cations are represented as dashed lanes. Coordinates of TREX1 --dTMP --Mg were taken from the PDB code 2O4G. (E) Diagrams showing distances (in angstroms) and B-factors (in parentheses) for each ion in position A in the active center.

Figure 4.
Histidine 124 in the inhibited and active complexes including the structure with single-stranded DNA. Active-site superimposition of the inhibited sodium complex (gray) with (A) the catalytic magnesium complex (blue) and (B) the TREX1 --ssDNA complex (blue). The protein residues and the dTMP molecule are labeled and represented as atom-type sticks. The metal-binding sites A and B are also indicated, and the spheres representing the ions are labeled in green (magnesium), orange (sodium), and magenta (undetermined metal). Distances between His124 and Ser155 are clearly indicated. Coordinates of TREX1 --ssDNA were taken from the PDB code 2O4I.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2008, 17, 2059-2069) copyright 2008.

Figures were selected by an automated process.