PDBsum entry 5dbb

Transferase/DNA

PDB id: 5dbb

Contents

Protein chain

327 a.a.

DNA/RNA

Metals

_NA ×2

Waters ×163

PDB id:

5dbb

Name:

Transferase/DNA

Title:

Structure of human DNA polymerase beta host-guest complex with the dg base paired with a da

Structure:

DNA polymerase beta. Chain: a. Engineered: yes. DNA (5'-d( Cp Cp Gp Ap Cp Gp Tp Cp Gp Cp Ap Tp Ap Ap Gp C)- 3'). Chain: t. Engineered: yes. DNA (5'-d( Gp Cp Tp Gp Ap Tp Gp Cp Gp A)-3'). Chain: p.

Source:

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

Resolution:

2.25Å R-factor: 0.209 R-free: 0.265

Authors:

M.C.Koag,S.Lee

Key ref:

Y.Kou et al. (2015). N7 methylation alters hydrogen-bonding patterns of guanine in duplex DNA. J Am Chem Soc, 137, 14067-14070. PubMed id: 26517568 DOI: 10.1021/jacs.5b10172

Date:

21-Aug-15 Release date: 11-Nov-15

Protein chain

P06746  (DPOLB_HUMAN) -  DNA polymerase beta from Homo sapiens

Seq: 335 a.a.

Struc: 327 a.a.

DNA/RNA chains

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

G-C-T-G-A-T-G-C-G-A 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: 10.1021/jacs.5b10172

J Am Chem Soc 137:14067-14070 (2015)

PubMed id: 26517568

N7 methylation alters hydrogen-bonding patterns of guanine in duplex DNA.

Y.Kou, M.C.Koag, S.Lee.

ABSTRACT

N7-Alkyl-2'-deoxyguanosines are major adducts in DNA that are generated by various alkylating mutagens and drugs. However, the effect of the N7 alkylation on the hydrogen-bonding patterns of the guanine remains poorly understood. We prepared N7-methyl-2'-deoxyguanosine (N7mdG)-containing DNA using a transition-state destabilization strategy, developed a novel polβ-host-guest complex system, and determined eight crystal structures of N7mdG or dG paired with dC, dT, dG, and dA. The structures of N7mdG:dC and N7mdG:dG are very similar to those of dG:dC and dG:dG, respectively, indicating the involvement of the keto tautomeric form of N7mdG in the base pairings with dC and dG. On the other hand, the structure of N7mdG:dT shows that the mispair forms three hydrogen bonds and adopts a Watson-Crick-like geometry rather than a wobble geometry, suggesting that the enol tautomeric form of N7mdG involves in its base pairing with dT. In addition, N7mdG:dA adopts a novel shifted anti:syn base pair presumably via the enol tautomeric form of N7mdG. The polβ-host-guest complex structures reveal that guanine-N7 methylation changes the hydrogen-bonding patterns of the guanine when paired with dT or dA and suggest that N7 alkylation may alter the base pairing patterns of guanine by promoting the formation of the rare enol tautomeric form of guanine.