PDBsum entry 1mq3

Transferase/DNA

PDB id: 1mq3

Contents

Protein chain

326 a.a. *

DNA/RNA

Ligands

DCP

Metals

_MG

_NA ×2

Waters ×78

* Residue conservation analysis

PDB id:

1mq3

Name:

Transferase/DNA

Title:

Human DNA polymerase beta complexed with gapped DNA containing an 8- oxo-7,8-dihydro-guanine template paired with dctp

Structure:

5'-d( Cp Cp Gp Ap Cp (8Og)p Gp Cp Gp Cp Ap Tp Cp Ap Gp C)- 3'. Chain: t. Engineered: yes. 5'-d( Gp Cp Tp Gp Ap Tp Gp Cp Gp (Doc))-3'. Chain: p. Engineered: yes. 5'-d(p Gp Tp Cp Gp G)-3'. Chain: d.

Source:

Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Tetramer (from PQS)

Resolution:

2.80Å R-factor: 0.235 R-free: 0.295

Authors:

J.M.Krahn,W.A.Beard,H.Miller,A.P.Grollman,S.H.Wilson

Key ref:

J.M.Krahn et al. (2003). Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential. Structure, 11, 121-127. PubMed id: 12517346 DOI: 10.1016/S0969-2126(02)00930-9

Date:

13-Sep-02 Release date: 28-Jan-03

Protein chain

P06746  (DPOLB_HUMAN) -  DNA polymerase beta from Homo sapiens

Seq: 335 a.a.

Struc: 326 a.a.

DNA/RNA chains

C-C-G-A-C-8OG-G-C-G-C-A-T-C-A-G-C 16 bases

G-C-T-G-A-T-G-C-G-DOC 10 bases

G-T-C-G-G 5 bases

Enzyme reactions

• Enzyme class 1: 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: E.C.4.2.99.- - ?????
• Enzyme class 3: E.C.4.2.99.18 - DNA-(apurinic or apyrimidinic site) lyase.
• Reaction: 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + H⁺

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: 10.1016/S0969-2126(02)00930-9

Structure 11:121-127 (2003)

PubMed id: 12517346

Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential.

J.M.Krahn, W.A.Beard, H.Miller, A.P.Grollman, S.H.Wilson.

ABSTRACT

Oxidative damage to DNA generates 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG). During DNA replication and repair synthesis, 8-oxodG can pair with cytosine or adenine. The ability to accurately replicate through this lesion depends on the DNA polymerase. We report the first structure of a polymerase with a promutagenic DNA lesion, 8-oxodG, in the confines of its active site. The modified guanine residue is in an anti conformation and forms Watson-Crick hydrogen bonds with an incoming dCTP. To accommodate the oxygen at C8, the 5'-phosphate backbone of the templating nucleotide flips 180 degrees. Thus, the flexibility of the template sugar-phosphate backbone near the polymerase active site is one parameter that influences the anti-syn equilibrium of 8-oxodG. Our results provide insights into the mechanisms employed by polymerases to select the complementary dNTP.

Selected figure(s)

Figure 3.
Figure 3. DNA Polymerase b Ternary Complex with 8-OxodG-dCTP(A) 2F[o] - F[c] electron density map contoured at 1 s (black), superimposed on the refined model. Additionally, a difference map was calculated, omitting O8 and contoured at 3.3 s. Negative density (red) is visible at the 8-oxy position of the template base, demonstrating unbiased evidence of the presence of the additional oxygen. The ternary complex with an 8-oxodG template base is very similar to the previously determined ternary complex containing undamaged deoxyguanine paired with ddCTP [12]. The modified guanine is in the standard anti conformation, and dCTP is bound with a coordinating Mg2+ atom (data not shown).(B) Comparison of the 5'-phosphate backbone conformation of 8-oxodG relative to that observed in the structure of pol b with an unmodified deoxyguanine in the polymerase active site (orange) [12]. The presence of the sharp bend along with limited enzyme contacts with this phosphate enables flipping of the phosphate away from the carbonyl oxygen at C8 of 8-oxodG. The backbone a torsion angle (O3'-P-O5'-C5') of the templating guanine is altered 184° when a carbonyl group is introduced at C8. In addition, the Lys280 side chain position, but not that of Asp276, is altered in the presence of 8-oxodG.

The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 121-127) copyright 2003.

Figure was selected by the author.