PDBsum entry: 2dy4

Transferase/DNA

PDB-id: 2dy4

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Description

Header details

Header records

References

PROCHECK

Protein chains

902 a.a. *

DNA/RNA

Waters ×606

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

2dy4

Name:

Transferase/DNA

Title:

Crystal structure of rb69 gp43 in complex with DNA containing thymine glycol

Structure:

5'-d( Cp Gp (Ctg) p Gp Gp Ap Ap Tp Gp A Cp Ap Gp Cp Cp Gp Cp G)-3'. Chain: e, g, i, k. Engineered: yes. 5'- d( Gp Cp Gp Gp Cp Tp Gp T Cp Ap Tp Tp Cp Cp A)-3'. Chain: f, h, j, l. Engineered: yes. DNA polymerase.

Source:

Synthetic: yes. Enterobacteria phage rb69. Organism_taxid: 12353. Gene: gp43. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

UniProt:

Chains A, B, C, D: Q38087 (DPOL_BPR69)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

903 a.a.

Struc:

902 a.a.*

Key:

PfamA domain

Secondary structure

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme class:

E.C.2.7.7.7   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (see diagram below)

Resolution:

2.65Å

R-factor:

0.229

R-free:

0.281

Authors:

P.Aller,M.A.Rould,M.Hogg,S.S.Wallace,S.Doublie

Key ref:

P.Aller et al. (2007). A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol.. Proc Natl Acad Sci U S A, 104, 814-818. [PubMed id: 17210917] [DOI: 10.1073/pnas.0606648104]

Date:

06-Sep-06

Release date:

09-Jan-07

Related entries:

1clq
rb69 gp43 complexed with undamaged DNA in exonuclease
active site
1ig9
rb69 gp43 complexed with undamaged DNA in exonuclease
active site
1rv2
rb69 gp43 complexed with DNA containing an abasic site
analog
1q9x
... plus others (see Header records)

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Key reference

DOI no: 10.1073/pnas.0606648104

Proc Natl Acad Sci U S A 104:814-818 (2007)

PubMed id: 17210917

A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol.

P.Aller, M.A.Rould, M.Hogg, S.S.Wallace, S.Doublié.

ABSTRACT

Thymine glycol (Tg) is a common product of oxidation and ionizing radiation, including that used for cancer treatment. Although Tg is a poor mutagenic lesion, it has been shown to present a strong block to both repair and replicative DNA polymerases. The 2.65-A crystal structure of a binary complex of the replicative RB69 DNA polymerase with DNA shows that the templating Tg is intrahelical and forms a regular Watson-Crick base pair with the incorporated A. The C5 methyl group protrudes axially from the ring of the damaged pyrimidine and hinders stacking of the adjacent 5' template guanine. The position of the displaced 5' template guanine is such that the next incoming nucleotide cannot be incorporated into the growing primer strand, and it explains why primer extension past the lesion is prohibited even though DNA polymerases can readily incorporate an A across from the Tg lesion.

Selected figure(s)

Figure 1.
Fig. 1. Tg is the product of ionizing radiation and oxidation. -irradiation produces equal amounts of the (5R, 6S) and (5S, 6R) cis isomers, whereas oxidation generates preferentially the (5R, 6S) isomer.

Figure 5.
Fig. 5. Interaction of Tg with surrounding bases. Superposition of the Tg·acyAMP complex (green) with an incipient base pair (A·dTTP) from an RB69 gp43 complex with normal DNA (29) (yellow; PDB ID code 1IG9). The adenine (yellow) overlaid on the Tg·acyAMP structure (green) illustrates that the methyl group of Tg would sterically clash with the six-member ring of any purine base in the insertion site (i). The displaced 5'-guanine (green) rotates out of the way and is stabilized by two hydrogen bonds with Tg. Tg also interacts with the 3'-guanine via a water-mediated interaction. Water molecules are shown as red spheres.

Figures were selected by the author.