PDBsum entry 4z6f

Transferase/DNA

PDB id: 4z6f

Contents

Protein chain

326 a.a.

DNA/RNA

Ligands

1FZ

Metals

_MN ×2

_NA ×2

Waters ×79

PDB id:

4z6f

Name:

Transferase/DNA

Title:

Structure of human DNA polymerase beta 279na mutant complexed with g in the template base paired with incoming non-hydrolyzable ttp and manganese

Structure:

DNA polymerase beta. Chain: a. Fragment: unp residues 10-335. Engineered: yes. DNA (5'-d( Cp Cp Gp Ap Cp (6Og) p Tp Cp Gp Cp Ap Tp Cp Ap Gp C)-3'). Chain: t. Engineered: yes. DNA (5'-d( Gp Cp Tp Gp Ap Tp Gp Cp Gp A)-3').

Source:

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

Resolution:

2.44Å R-factor: 0.198 R-free: 0.248

Authors:

M.-C.Koag,S.Lee

Key ref:

M.C.Koag and S.Lee (2018). Insights into the effect of minor groove interactions and metal cofactors on mutagenic replication by human DNA polymerase β. Biochem J, 475, 571-585. PubMed id: 29301983

Date:

04-Apr-15 Release date: 13-Apr-16

Protein chain

P06746  (DPOLB_HUMAN) -  DNA polymerase beta from Homo sapiens

Seq: 335 a.a.

Struc: 326 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

C-C-G-A-C-6OG-T-C-G-C-A-T-C-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

Biochem J 475:571-585 (2018)

PubMed id: 29301983

Insights into the effect of minor groove interactions and metal cofactors on mutagenic replication by human DNA polymerase β.

M.C.Koag, S.Lee.

ABSTRACT

DNA polymerases accommodate various base-pair conformations in the event of incorrect insertions. In particular, Watson-Crick-like dG:dTTP base pair has been observed at the insertion site of human DNA polymerase β (pol β). A potential factor contributing to the diverse conformations of base-pair mismatches is minor groove interactions. To gain insights into the effect of minor groove interactions on base-pair conformations, we generated an Asn279Ala polβ mutant that cannot make minor groove contacts with an incoming nucleotide. We conducted structural and kinetic studies of Asn279Ala polβ in complex with incoming dTTP and templating dG or O6-methyl-dG. The crystal structure of the Asn279Ala polβ-G:T complex showed a wobble dG:dTTP base pair, indicating that the previously observed Watson-Crick-like dG:dTTP conformation was induced by the minor groove contact. In contrast, O6-methyl-dG, an analog of the enol tautomer of guanine, formed a Watson-Crick-like base pair with dTTP in the absence of the minor groove contact. These results suggest that the Watson-Crick-like G:T base pair at the insertion site is formed by the rare enol tautomers of G or T, whose population is increased by the minor groove hydrogen bond with Asn279. Kinetic studies showed that Asn279Ala mutation decreased dG:dTTP misincorporation rate six-fold in the presence of Mg²⁺ but increased the rate three-fold in the presence of Mn²⁺, highlighting the effect of minor groove interactions and metal ions on promutagenic replication by polβ.