PDBsum entry 1pm0

Transferase/DNA

PDB id: 1pm0

Contents

Protein chain

341 a.a.

DNA/RNA

Ligands

ATP

Metals

_CA ×2

Waters ×204

Obsolete entry

PDB id:

1pm0

Name:

Transferase/DNA

Title:

Replication of a cis-syn thymine dimer at atomic resolution

Structure:

DNA polymerase iv. Chain: a. Synonym: pol iv. Engineered: yes. 5'-d( Gp Gp Gp Gp Gp Ap Ap Gp Gp Ap Tp Tp C)-3'. Chain: b. Engineered: yes. 5'- d( Tp Tp Tp Gp Ap Ap Tp Cp Cp Tp Tp Cp Cp Cp Cp C)-3'.

Source:

Sulfolobus solfataricus. Archaea. Gene: dpo4. Expressed in: escherichia coli. Synthetic: yes. Synthetic: yes

Biol. unit:

Trimer (from PQS)

Resolution:

2.28Å R-factor: 0.253 R-free: 0.281

Authors:

H.Ling,F.Boudsocq,B.Plosky,R.Woodgate,W.Yang

Key ref:

H.Ling et al. (2003). Replication of a cis-syn thymine dimer at atomic resolution. Nature, 424, 1083-1087. PubMed id: 12904819 DOI: 10.1038/nature01919

Date:

09-Jun-03 Release date: 16-Sep-03

Protein chain

Q97W02  (DPO4_SULSO) -  DNA polymerase IV from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 352 a.a.

Struc: 341 a.a.

DNA/RNA chains

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

T-T-T-G-A-A-T-C-C-T-T-C-C-C-C-C 16 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

DNA(n) (Bound ligand (Het Group name = ATP) matches with 6129.00% similarity corresponds exactly) + 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

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

Added reference

DOI no: 10.1038/nature01919

Nature 424:1083-1087 (2003)

PubMed id: 12904819

Replication of a cis-syn thymine dimer at atomic resolution.

H.Ling, F.Boudsocq, B.S.Plosky, R.Woodgate, W.Yang.

ABSTRACT

Ultraviolet light damages DNA by catalysing covalent bond formation between adjacent pyrimidines, generating cis-syn cyclobutane pyrimidine dimers (CPDs) as the most common lesion. CPDs block DNA replication by high-fidelity DNA polymerases, but they can be efficiently bypassed by the Y-family DNA polymerase pol eta. Mutations in POLH encoding pol eta are implicated in nearly 20% of xeroderma pigmentosum, a human disease characterized by extreme sensitivity to sunlight and predisposition to skin cancer. Here we have determined two crystal structures of Dpo4, an archaeal pol eta homologue, complexed with CPD-containing DNA, where the 3' and 5' thymine of the CPD separately serves as a templating base. The 3' thymine of the CPD forms a Watson-Crick base pair with the incoming dideoxyATP, but the 5' thymine forms a Hoogsteen base pair with the dideoxyATP in syn conformation. Dpo4 retains a similar tertiary structure, but each unusual DNA structure is individually fitted into the active site for catalysis. A model of the pol eta-CPD complex built from the crystal structures of Saccharomyces cerevisiae apo-pol eta and the Dpo4-CPD complex suggests unique features that allow pol eta to efficiently bypass CPDs.

Selected figure(s)

Figure 1.
Figure 1: Replication of a CPD by Dpo4 in solution and crystals. a, Extension of two primers (13 nucleotides each) paired with undamaged or CPD-containing 18-nucleotide templates used in the crystallization studies (TT-1, TT-2). Reactions were carried out with 10 nM DNA substrate, 10 nM Dpo4 and 100 M dATP at 37 °C for 2, 5, 10 or 20 min. b, Inhibition of primer extension by ddATP. P indicates primer strand, and U and D indicate undamaged and CPD-containing template, respectively. The reactions took place for 30 min at 22 °C or 37 °C as indicated. c, The active site of TT-1, where the 3' thymine of the CPD (orange) is base-paired with ddATP (yellow). The conserved residues interacting with ddATP and catalytic carboxylates are highlighted. Tyr 10, which immobilizes the finger domain by wedging between the palm and finger domains, is shown in red. d, Replication at the 3' T of the CPD. The CPD and the replicating and preceding base pairs of TT-1 are shown with the F[o] - F[c] omit electron densities. e, Active site of TT-2, where the 5' thymine of the CPD is base-paired with ddATP, f, The replicating and two preceding base pairs of the TT-2 are shown with the F[o] - F[c] omit electron densities. g, Stereo view of the TT-1 (blue) and TT-2 (pink) active-site superposition. The three catalytic carboxylates, two Ca^2+ ions, the 3' nucleotide of the primer strand, and the incoming nucleotide are shown in the ball-and-stick model.

Figure 2.
Figure 2: Structural comparison of the CPD complexed with Dpo4 and protein free. a, Structures of the CPD (orange) and surrounding nucleic acids in TT-1 (blue), TT-2 (pink) and in the absence of protein (yellow)19 are shown in the ball-and-stick model after superposition of the CPDs. b, c, Ball-and-stick presentations of base-pairing of the CPDs in TT-1 (b) and TT-2 (c). The phosphorus atoms are shown in purple, oxygen in red and nitrogen in dark blue. The carbon atoms of the replicating base pair are white, and others are light blue.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2003, 424, 1083-1087) copyright 2003.

Figures were selected by an automated process.