Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 70716.69 
• Atom Count: 4797 
• Residue Count: 613 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2KZM

KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC AND MANGANESE

• DOI: 10.2210/pdb2KZM/pdb
• NDB: PD0105

• Classification: TRANSFERASE/DNA
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 1998-07-03 Released: 1999-02-16 
• Deposition Author(s): Brautigam, C.A., Sun, S., Piccirilli, J.A., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.243 
• R-Value Work: 0.195 

Literature

Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli.

Brautigam, C.A., Sun, S., Piccirilli, J.A., Steitz, T.A.

(1999) Biochemistry 38: 696-704

• PubMed: 9888810 
• DOI: 10.1021/bi981537g
• Primary Citation of Related Structures:  
  2KZZ, 2KFZ, 2KFN


• PubMed Abstract: 
  

The interaction of a divalent metal ion with a leaving 3' oxygen is a central component of several proposed mechanisms of phosphoryl transfer. In support of this are recent kinetic studies showing that thiophilic metal ions (e.g., Mn2+) stimulate the hydrolysis of compounds in which sulfur takes the place of the leaving oxygen. To examine the structural basis of this phenomenon, we have solved four crystal structures of single-stranded DNA's containing either oxygen or sulfur at a 3'-bridging position bound in conjunction with various metal ions at the 3'-5' exonucleolytic active site of the Klenow fragment (KF) of DNA polymerase I from Escherichia coli. Two structures of normal ssDNA bound to KF in the presence of Zn2+ and Mn2+ or Zn2+ alone were refined at 2.6- and 2.25-A resolution, respectively. They serve as standards for comparison with other Mn2+- and Zn2+-containing structures. In these cases, Mn2+ and Zn2+ bind at metal ion site B in a nearly identical position to Mg2+ (Brautigam and Steitz (1998) J. Mol. Biol. 277, 363-377). Two structures of KF bound to a deoxyoligonucleotide that contained a 3'-bridging sulfur at the scissile phosphate were refined at 2.03-A resolution. Although the bridging sulfur compounds bind in a manner very similar to that of the normal oligonucleotides, the presence of the sulfur changes the metal ion binding properties of the active site such that Mn2+ and Zn2+ are observed at metal ion site B, but Mg2+ is not. It therefore appears that the ability of the bridging sulfur compounds to exclude nonthiophilic metal ions from metal ion site B explains the low activity of KF exonuclease on these substrates in the presence of Mg2+ (Curley et al. (1997) J. Am. Chem. Soc. 119, 12691-12692) and that the 3'-bridging atom of the substrate is influencing the binding of metal ion B prior to catalysis.

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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




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (DNA POLYMERASE I)	A	605	Escherichia coli (strain K12)	Mutation(s): 1  Gene Names: polA (resA) EC: 2.7.7.7
Find proteins for P00582 (Escherichia coli (strain K12)) Go to UniProtKB:  P00582

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MN	B	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.243 
• R-Value Work: 0.195 
• Space Group: P 4₃

Unit Cell:

Length (Å)	Angle (°)
a = 102.600	α = 90.00
b = 102.600	β = 90.00
c = 86.200	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-07-03 
• Released Date: 1999-02-16 
• Deposition Author(s): Brautigam, C.A., Sun, S., Piccirilli, J.A., Steitz, T.A.

Revision History 

• Version 1.0: 1999-02-16
  Type: Initial release
• Version 1.1: 2008-05-22
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance