PDBsum entry 3isc

Transferase/DNA

PDB id: 3isc

Contents

Protein chain

327 a.a. *

DNA/RNA

Metals

_NA ×4

Waters ×511

* Residue conservation analysis

PDB id:

3isc

Name:

Transferase/DNA

Title:

Binary complex of human DNA polymerase beta with an abasic site (thf) in the gapped DNA

Structure:

DNA polymerase beta. Chain: a. Engineered: yes. 5'-d(p Gp Tp Cp Gp G)-3'. Chain: d. Engineered: yes. 5'-d( Gp Cp Tp Gp Ap Tp Gp Cp Gp C)-3'. Chain: p. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

2.00Å R-factor: 0.186 R-free: 0.227

Authors:

W.A.Beard,D.D.Shock,V.K.Batra,L.C.Pedersen,S.H.Wilson

Key ref:

W.A.Beard et al. (2009). DNA polymerase beta substrate specificity: side chain modulation of the "A-rule". J Biol Chem, 284, 31680-31689. PubMed id: 19759017

Date:

25-Aug-09 Release date: 15-Sep-09

Protein chain

P06746  (DPOLB_HUMAN) -  DNA polymerase beta from Homo sapiens

Seq: 335 a.a.

Struc: 327 a.a.

DNA/RNA chains

G-T-C-G-G 5 bases

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

C-C-G-A-C-3DR-G-C-G-C-A-T-C-A-G-C 16 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

J Biol Chem 284:31680-31689 (2009)

PubMed id: 19759017

DNA polymerase beta substrate specificity: side chain modulation of the "A-rule".

W.A.Beard, D.D.Shock, V.K.Batra, L.C.Pedersen, S.H.Wilson.

ABSTRACT

Apurinic/apyrimidinic (AP) sites are continuously generated in genomic DNA. Left unrepaired, AP sites represent noninstructional premutagenic lesions that are impediments to DNA synthesis. When DNA polymerases encounter an AP site, they generally insert dAMP. This preferential insertion is referred to as the A-rule. Crystallographic structures of DNA polymerase (pol) beta, a family X polymerase, with active site mismatched nascent base pairs indicate that the templating (i.e. coding) base is repositioned outside of the template binding pocket thereby diminishing interactions with the incorrect incoming nucleotide. This effectively produces an abasic site because the template pocket is devoid of an instructional base. However, the template pocket is not empty; an arginine residue (Arg-283) occupies the space vacated by the templating nucleotide. In this study, we analyze the kinetics of pol beta insertion opposite an AP site and show that the preferential incorporation of dAMP is lost with the R283A mutant. The crystallographic structures of pol beta bound to gapped DNA with an AP site analog (tertrahydrofuran) in the gap (binary complex) and with an incoming nonhydrolyzable dATP analog (ternary complex) were solved. These structures reveal that binding of the dATP analog induces a closed polymerase conformation, an unstable primer terminus, and an upstream shift of the templating residue even in the absence of a template base. Thus, dATP insertion opposite an abasic site and dATP misinsertions have common features.