1EXN

T5 5'-EXONUCLEASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease.

Ceska, T.A.Sayers, J.R.Stier, G.Suck, D.

(1996) Nature 382: 90-93

  • DOI: 10.1038/382090a0

  • PubMed Abstract: 
  • THE 5'-exonucleases are enzymes that are essential for DNA replication and repair. As well as their exonucleolytic action, removing nucleotides from the 5'-end of nucleic acid molecules such as Okazaki fragments, many 5'-3'-exonucleases have been sho ...

    THE 5'-exonucleases are enzymes that are essential for DNA replication and repair. As well as their exonucleolytic action, removing nucleotides from the 5'-end of nucleic acid molecules such as Okazaki fragments, many 5'-3'-exonucleases have been shown to possess endonucleolytic activities. T5 5'-3'-exonuclease shares many similarities with the amino terminal of eubacterial DNA polymerases, although, unlike eubacteria, phages such as T5, T4 and T7 express polymerase and 5'-exonuclease proteins from separate genes. Here we report the 2.5-A crystal structure of the phage T5 5'-exonuclease, which reveals a helical arch for binding DNA. We propose a model consistent with a threading mechanism in which single-stranded DNA could slide through the arch, which is formed by two helices, one containing positively charged, and the other hydrophobic, residues. The active site is at the base of the arch, and contains two metal-binding sites.


    Related Citations: 
    • Properties of Overexpressed Phage T5 D15 Exonuclease. Similarities with Escherichia Coli DNA Polymerase I 5'-3' Exonuclease
      Sayers, J.R.,Eckstein, F.
      (1990) J.Biol.Chem. 265: 18311
    • Preliminary Crystallographic Studies on the D15 5' to 3' Exonuclease from Phage T5
      Ceska, T.A.,Sayers, J.R.,Eckstein, F.,Suck, D.
      (1993) J.Mol.Biol. 233: 179


    Organizational Affiliation

    EMBL, Structural Biology Programme, Heidelberg, Germany. ceska@embl.heidelbergde




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-EXONUCLEASE
A, B
290Escherichia phage T5Gene Names: D15 (exo5)
EC: 3.1.11.3, 3.1.11.-
Find proteins for P06229 (Escherichia phage T5)
Go to UniProtKB:  P06229
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.227 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 77.760α = 90.00
b = 77.760β = 90.00
c = 134.690γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-07-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance