1QSL

KLENOW FRAGMENT COMPLEXED WITH SINGLE-STRANDED SUBSTRATE AND EUROPIUM (III) ION

• PDB DOI:  https://doi.org/10.2210/pdb1QSL/pdb
• NAKB: 1QSL

• Classification: TRANSFERASE/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-06-22 Released: 1999-06-30 
• Deposition Author(s): Brautigam, C.A., Aschheim, K., Steitz, T.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.255 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 

Literature

Structural elucidation of the binding and inhibitory properties of lanthanide (III) ions at the 3'-5' exonucleolytic active site of the Klenow fragment

Brautigam, C.A., Aschheim, K., Steitz, T.A.

(1999) Chem Biol 6: 901-908

• PubMed: 10631518 
• DOI: https://doi.org/10.1016/s1074-5521(00)80009-5
• Primary Citation of Related Structures:  
  1QSL


• PubMed Abstract: 
  

Biochemical and biophysical experiments have shown that two catalytically essential divalent metal ions (termed 'A' and 'B') bind to the 3'-5' exonuclease active site of the Klenow fragment (KF) of Escherichia coli DNA polymerase I. X-ray crystallographic studies have established the normal positions in the KF 3'-5' exonuclease (KF exo) active site of the two cations and the single-stranded DNA substrate. Lanthanide (III) luminescence studies have demonstrated, however, that only a single europium (III) ion (Eu3+) binds to the KF exo active site. Furthermore, Eu3+ does not support catalysis by KF exo or several other two-metal-ion phosphoryl-transfer enzymes.

---

Related Citations: 

• Structural Principles for the Inhibition of the 3'-5' Exonuclease Activity of Escherichia Coli DNA Polymerase I by Phosphorothioates
  Brautigam, C.A., Steitz, T.A.
  (1998) J Mol Biol 277: 363

• Structural Basis for the 3'-5' Exonuclease Activity of Escherichia Coli DNA Polymerase I: A Two Metal Ion Mechanism
  Beese, L.S., Steitz, T.A.
  (1991) EMBO J 10: 25

---

Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 70.75 kDa 
• Atom Count: 5,006 
• Modelled Residue Count: 605 
• Deposited Residue Count: 613 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA POLYMERASE I	B [auth A]	605	Escherichia coli	Mutation(s): 1  EC: 2.7.7.7
UniProt
Find proteins for P00582 (Escherichia coli (strain K12)) Explore P00582  Go to UniProtKB:  P00582

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*TP*TP*AP*CP*GP*C)-3'	A [auth B]	8	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EU	C [auth A]	EUROPIUM ION Eu MGVUQZZTJGLWJV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.255 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.3	α = 90
b = 103.3	β = 90
c = 86.5	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-06-30 
Deposition Author(s): Brautigam, C.A., Aschheim, K., Steitz, T.A.

Revision History  

• Version 1.0: 1999-06-30
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations