1KLN | pdb_00001kln

DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7) MUTANT/DNA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1KLN/pdb
• NAKB: 1KLN

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


• Deposited: 1994-05-24 Released: 1994-11-30 
• Deposition Author(s): Beese, L.S., Derbyshire, V., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Work: 
  0.230 (Depositor) 

Literature

Structure of DNA polymerase I Klenow fragment bound to duplex DNA.

Beese, L.S., Derbyshire, V., Steitz, T.A.

(1993) Science 260: 352-355

• PubMed: 8469987 
• DOI: https://doi.org/10.1126/science.8469987
• Primary Citation Related Structures: 
  1KLN


• PubMed Abstract: 
  

  Klenow fragment of Escherichia coli DNA polymerase I, which was cocrystallized with duplex DNA, positioned 11 base pairs of DNA in a groove that lies at right angles to the cleft that contains the polymerase active site and is adjacent to the 3' to 5' exonuclease domain. When the fragment bound DNA, a region previously referred to as the "disordered domain" became more ordered and moved along with two helices toward the 3' to 5' exonuclease domain to form the binding groove. A single-stranded, 3' extension of three nucleotides bound to the 3' to 5' exonuclease active site. Although this cocrystal structure appears to be an editing complex, it suggests that the primer strand approaches the catalytic site of the polymerase from the direction of the 3' to 5' exonuclease domain and that the duplex DNA product may bend to enter the cleft that contains the polymerase catalytic site.

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Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 75.22 kDa 
• Atom Count: 5,140 
• Modeled Residue Count: 618 
• Deposited Residue Count: 628 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7))	C [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
DNA (5'-D(*GP*CP*CP*TP*CP*GP*CP*GP*GP*CP*GP*GP*C)-3')	A [auth B]	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*CP*GP*CP*GP*AP*GP*GP*C)-3')	B [auth C]	10	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Work:  0.230 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.3	α = 90
b = 104.3	β = 90
c = 86	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-11-30 
Deposition Author(s): Beese, L.S., Derbyshire, V., Steitz, T.A.

Revision History  

• Version 1.0: 1994-11-30
  Type: Initial release
  
• Version 1.1: 2008-05-22
  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
• Version 1.4: 2024-02-14
  Changes: Data collection