PDBsum entry: 1ir6

Hydrolase

PDB id: 1ir6

Contents

Protein chain

385 a.a. *

Metals

_MN

* Residue conservation analysis

PDB id:

1ir6

Name:

Hydrolase

Title:

Crystal structure of exonuclease recj bound to manganese

Structure:

Exonuclease recj. Chain: a. Fragment: catalytic domain. Synonym: single-stranded DNA specific exonuclease recj. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PQS)

Resolution:

2.90Å R-factor: 0.228 R-free: 0.259

Authors:

A.Yamagata,Y.Kakuta,R.Masui,K.Fukuyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

A.Yamagata et al. (2002). The crystal structure of exonuclease RecJ bound to Mn2+ ion suggests how its characteristic motifs are involved in exonuclease activity. Proc Natl Acad Sci U S A, 99, 5908-5912. PubMed id: 11972066 DOI: 10.1073/pnas.092547099

Date:

11-Sep-01 Release date: 15-May-02

Protein chain

Q93R48  (Q93R48_THETH) -  Single-stranded DNA specific exonuclease RecJ

Seq: 666 a.a.

Struc: 385 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (3 terms)

DOI no: 10.1073/pnas.092547099

Proc Natl Acad Sci U S A 99:5908-5912 (2002)

PubMed id: 11972066

The crystal structure of exonuclease RecJ bound to Mn2+ ion suggests how its characteristic motifs are involved in exonuclease activity.

A.Yamagata, Y.Kakuta, R.Masui, K.Fukuyama.

ABSTRACT

RecJ, a 5' to 3' exonuclease specific for single-stranded DNA, functions in DNA repair and recombination systems. We determined the crystal structure of RecJ bound to Mn(2+) ion essential for its activity. RecJ has a novel fold in which two domains are interconnected by a long helix, forming a central groove. Mn(2+) is located on the wall of the groove and is coordinated by conserved residues characteristic of a family of phosphoesterases that includes RecJ proteins. The groove is composed of residues conserved among RecJ proteins and is positively charged. These findings and the narrow width of the groove indicate that the groove binds single- instead of double-stranded DNA.

Selected figure(s)

Figure 1.
Fig. 1. The RecJ structure. (a, b) Ribbon diagrams of RecJ. b is viewed at an orientation rotated 90° from a. -strands in domain I are shown in cyan; -helices in the / structure in domain I, blue; -helices in the helix-rich region in domain I, green; -strands in domain II, orange; -helices in domain II, red; and 12, yellow. The Mn2+ ion is shown by a magenta ball. The side chains of the residues bound to Mn2+ are indicated by a stick model. (c) The Mn2+-binding site. The electron density (green) of the Mn2+ ion derived from the Bijvoet difference ( = 1.8808 Å) is superimposed on the model. The position of the Mn2+ ion is shown by a magenta ball. The distances to Mn2+ are Asp-82, 4.55 and 4.68 Å; Asp-84, 2.39 Å; Asp-136, 2.64, and 2.63 Å; His-160, 2.24 Å; His-161, 3.22 Å; and Asp-221, 2.50 Å. a and b were drawn with MOLSCRIPT (31) and RASTER 3D (32), c with O (14) and MOLRAY (33).

Figure 3.
Fig. 3. Conserved residues and the electrostatic surface of RecJ. (a) Orthogonal views of the CPK model of RecJ. The left and right views are in the same respective orientations as in Fig. 1 a and b. The extent of conservation is indicated by differences in the shades of blue, as described in Fig. 2. The NH[ ]group of the Arg residue and NH[2] group of the Asn and Gln residues, which are available for ssDNA binding, are shown in purple. (b) The electrostatic surface potential of RecJ viewed from the same orientation as in Fig. 1a. These figures were drawn with GRASP (35).

Figures were selected by an automated process.