1EXN

T5 5'-EXONUCLEASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  
    1EXN

  • 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 shown to possess endonucleolytic activities ...

    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: 
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5'-EXONUCLEASE AB290Escherichia virus T5Mutation(s): 4 
Gene Names: D15exo5T5.130T5p128
EC: 3.1.11.3 (PDB Primary Data), 3.1.11 (UniProt)
Find proteins for P06229 (Escherichia phage T5)
Explore P06229 
Go to UniProtKB:  P06229
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.76α = 90
b = 77.76β = 90
c = 134.69γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-07-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-11
    Changes: Data collection, Other