PDBsum entry 1nke

Transferase/DNA

PDB id: 1nke

Contents

Protein chain

580 a.a. *

DNA/RNA

Ligands

GLC-FRU ×2

DCP

SO4 ×5

Metals

_MG

Waters ×441

* Residue conservation analysis

PDB id:

1nke

Name:

Transferase/DNA

Title:

A bacillus DNA polymerase i product complex bound to a cytosine- thymine mismatch after a single round of primer extension, following incorporation of dctp.

Structure:

DNA primer strand. Chain: b. Engineered: yes. DNA template strand. Chain: c. Engineered: yes. DNA polymerase i. Chain: a. Fragment: bacillus fragment (analogous to the e. Coli klenow

Source:

Synthetic: yes. Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PQS)

Resolution:

1.80Å R-factor: 0.216 R-free: 0.248

Authors:

S.J.Johnson,L.S.Beese

Key ref:

S.J.Johnson and L.S.Beese (2004). Structures of mismatch replication errors observed in a DNA polymerase. Cell, 116, 803-816. PubMed id: 15035983 DOI: 10.1016/S0092-8674(04)00252-1

Date:

02-Jan-03 Release date: 30-Mar-04

Protein chain

P52026  (DPO1_GEOSE) -  DNA polymerase I from Geobacillus stearothermophilus

Seq: 876 a.a.

Struc: 580 a.a.*

* PDB and UniProt seqs differ at 67 residue positions (black crosses)

DNA/RNA chains

G-C-G-A-T-C-A-G-C-C-C 11 bases

G-T-G-C-T-G-A-T-C-G-C-A 12 bases

Enzyme reactions

• Enzyme class: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/S0092-8674(04)00252-1

Cell 116:803-816 (2004)

PubMed id: 15035983

Structures of mismatch replication errors observed in a DNA polymerase.

S.J.Johnson, L.S.Beese.

ABSTRACT

Accurate DNA replication is essential for genomic stability. One mechanism by which high-fidelity DNA polymerases maintain replication accuracy involves stalling of the polymerase in response to covalent incorporation of mismatched base pairs, thereby favoring subsequent mismatch excision. Some polymerases retain a "short-term memory" of replication errors, responding to mismatches up to four base pairs in from the primer terminus. Here we a present a structural characterization of all 12 possible mismatches captured at the growing primer terminus in the active site of a polymerase. Our observations suggest four mechanisms that lead to mismatch-induced stalling of the polymerase. Furthermore, we have observed the effects of extending a mismatch up to six base pairs from the primer terminus and find that long-range distortions in the DNA transmit the presence of the mismatch back to the enzyme active site, suggesting the structural basis for the short-term memory of replication errors.

Selected figure(s)

Figure 2.
Figure 2. DNA Mismatches Bound at the Polymerase Postinsertion SiteThe bases are shown in the same orientation and location as the G•C base pair in Figure 1B. Left, hydrogen bonding pattern. Right, superimposition of the molecular surface of the mismatch (red) and cognate G•C base pair (yellow, PDB ID 1L3S) bound at the postinsertion site, highlighting differences in shape and location of the primer terminus.

Figure 4.
Figure 4. Extension of a G•T Mismatch by Successive Rounds of ReplicationThe conformation of the G•T mismatch is shown at each position (left), including interacting water molecules (red spheres). Dashed lines indicate potential hydrogen bonds. At the n-3 and n-4 positions, hydrogen bonds are shown between groups within the appropriate distance (≤3.2 Å) and correspond to tautomerization or ionization of one of the bases (see text). A schematic representation (right) of the mismatch complex, drawn and color coded as described in Figure 1, Figure 2 and Figure 3, indicates regions of the polymerase active site that are disrupted upon binding of the mismatch (red line). Mismatch binding at positions n-1 to n-4 along the DNA duplex binding region (gray) results in a distorted open conformation at the polymerase active site as described by mechanism 1 (Figure 3). The normal open conformation observed with homoduplexes is fully restored when the mismatch is bound at the n-6 position.

The above figures are reprinted by permission from Cell Press: Cell (2004, 116, 803-816) copyright 2004.

Figures were selected by an automated process.