PDBsum entry 2p5o

Transferase/DNA

PDB id: 2p5o

Contents

Protein chains

856 a.a. *

771 a.a. *

671 a.a. *

DNA/RNA

Waters ×495

* Residue conservation analysis

PDB id:

2p5o

Name:

Transferase/DNA

Title:

Crystal structure of rb69 gp43 in complex with DNA containing an abasic site analog

Structure:

Template DNA. Chain: e, g, i, k. Engineered: yes. Primer DNA. Chain: f, h, j, l. Engineered: yes. DNA polymerase. Chain: a, b, c, d. Synonym: gp43.

Source:

Synthetic: yes. Other_details: commercially produced. Enterobacteria phage rb69. Organism_taxid: 12353. Gene: 43. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.80Å R-factor: 0.245 R-free: 0.290

Authors:

M.Hogg,S.S.Wallace,S.Doublie

Key ref:

M.Hogg et al. (2004). Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site. EMBO J, 23, 1483-1493. PubMed id: 15057283 DOI: 10.1038/sj.emboj.7600150

Date:

15-Mar-07 Release date: 03-Apr-07

Supersedes:

1rv2

Protein chains

Q38087  (DPOL_BPR69) -  DNA-directed DNA polymerase from Escherichia phage RB69

Seq: 903 a.a.

Struc: 856 a.a.*

Protein chain

Q38087  (DPOL_BPR69) -  DNA-directed DNA polymerase from Escherichia phage RB69

Seq: 903 a.a.

Struc: 771 a.a.*

Protein chain

Q38087  (DPOL_BPR69) -  DNA-directed DNA polymerase from Escherichia phage RB69

Seq: 903 a.a.

Struc: 671 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

DNA/RNA chains

C-G-3DR-C-T-T-A-T-G-A-C-A-G-C-C-G-C-G 18 bases

G-C-G-G-C-T-G-T-C-A-T-A-A-G-A 15 bases

T-A-T-G-A-C-A-G-C-C-G-C-G 13 bases

G-C-G-G-C-T-G-T-C-A-T-A-A-G-A 15 bases

C-G-3DR-C-T-T-A-T-G-A-C-A-G-C-C-G-C-G 18 bases

G-C-G-G-C-T-G-T-C-A-T-A-A-G-A 15 bases

A-C-A-G-C-C-G-C-G 9 bases

G-C-G-G-C-T-G-T 8 bases

Enzyme reactions

• Enzyme class 1: Chains A, B, C, D: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 2: Chains A, B, C, D: E.C.3.1.11.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

Added reference

DOI no: 10.1038/sj.emboj.7600150

EMBO J 23:1483-1493 (2004)

PubMed id: 15057283

Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site.

M.Hogg, S.S.Wallace, S.Doublié.

ABSTRACT

Abasic sites are common DNA lesions, which are strong blocks to replicative polymerases and are potentially mutagenic when bypassed. We report here the 2.8 A structure of the bacteriophage RB69 replicative DNA polymerase attempting to process an abasic site analog. Four different complexes were captured in the crystal asymmetric unit: two have DNA in the polymerase active site whereas the other two molecules are in the exonuclease mode. When compared to complexes with undamaged DNA, the DNA surrounding the abasic site reveals distinct changes suggesting why the lesion is so poorly bypassed: the DNA in the polymerase active site has not translocated and is therefore stalled, precluding extension. All four molecules exhibit conformations that differ from the previously published structures. The polymerase incorporates dAMP across the lesion under crystallization conditions, indicating that the different conformations observed in the crystal may be part of the active site switching reaction pathway.

Selected figure(s)

Figure 2.
Figure 2 Protein/DNA contacts in polymerizing and editing conformations. (A) Polymerase mode. Hydrogen bond contacts less than 2.8 Å are represented by solid lines and those greater than 2.8 and less than 3.5 Å are shown with dashed lines. Residues in parentheses represent charge interactions longer than 3.5 Å. Wavy lines represent water-mediated contacts. Hydrophobic interactions are symbolized by dashed arcs. Contacts mediated by a nitrogen main-chain atom are indicated by the suffix 'N'. Protein residues are colored according to their domain location: exonuclease (cyan), N-terminal domain (orange), palm (red), thumb (green) and fingers (blue). Underlined residues are contacts in Pol1 that are absent in Pol2. (B) Exonuclease mode. All descriptions as above.

Figure 4.
Figure 4 Minor groove interactions are lost in furan-containing DNA. (A) Minor groove interactions in the active site of ternary complex (1IG9; Franklin et al, 2001). Hydrogen bonds are shown as dashed red lines. For clarity only the bases of the primer strand are shown. (B) Pol1, in the same orientation as the ternary complex in (A). All minor groove interactions seen in the ternary complex are lost. (C) Pol2, in the same orientation as in (A) and (B). The DNA shifts further away from the palm domain.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 1483-1493) copyright 2004.

Figures were selected by an automated process.