1EXN | pdb_00001exn

T5 5'-EXONUCLEASE

• PDB DOI: https://doi.org/10.2210/pdb1EXN/pdb

• Classification: NUCLEASE
• Organism(s): Tequintavirus T5
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1997-01-17 Released: 1997-07-07 
• Deposition Author(s): Ceska, T.A., Sayers, J.R., Stier, G., Suck, D.

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Experimental Data Snapshot

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

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

• PubMed: 8657312 
• DOI: https://doi.org/10.1038/382090a0
• Primary Citation 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. 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.

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Organizational Affiliation: 
• EMBL, Structural Biology Programme, Heidelberg, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 67.19 kDa 
• Atom Count: 4,624 
• Modeled Residue Count: 543 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-EXONUCLEASE	A, B	290	Tequintavirus T5	Mutation(s): 4  Gene Names: D15 EC: 3.1.11.3 (PDB Primary Data), 3.1.11 (UniProt)
UniProt
Find proteins for P06229 (Escherichia phage T5) Explore P06229  Go to UniProtKB:  P06229

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

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

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.76	α = 90
b = 77.76	β = 90
c = 134.69	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-07-07 
Deposition Author(s): Ceska, T.A., Sayers, J.R., Stier, G., Suck, D.

Revision History  

• 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
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary