2KZM

KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC AND MANGANESE

PDB DOI: 10.2210/pdb2KZM/pdb
NDB: PD0105

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.243
R-Value Work: 0.195
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: 10.1021/bi981537g
Primary Citation of Related Structures:
2KFN, 2KFZ, 2KZM, 2KZZ

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.

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

Organizational Affiliation:

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

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00582
Protein Feature View Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(GPCPTPTPACPGPC)-3')	A [auth B]	8	N/A
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Ligand Interaction