PDBsum entry 1zjn

DNA/lyase/transferase

PDB id: 1zjn

Contents

Protein chain

325 a.a. *

DNA/RNA

Ligands

DGT

Metals

_MG

_NA ×3

Waters ×82

* Residue conservation analysis

PDB id:

1zjn

Name:

DNA/lyase/transferase

Title:

Human DNA polymerase beta complexed with DNA containing an a-a mismatched primer terminus with dgtp

Structure:

D( Cp Cp Gp Ap Cp Cp Ap 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 A)-3'. Chain: p. Engineered: yes. 5'-d(p Gp Tp Cp Gp G)-3'. Chain: d. Engineered: yes.

Source:

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

Biol. unit:

Tetramer (from PQS)

Resolution:

2.61Å R-factor: 0.228 R-free: 0.234

Authors:

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

Key ref:

V.K.Batra et al. (2005). Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate. Structure (Camb), 13, 1225-1233. PubMed id: 16084394 DOI: 10.1016/j.str.2005.05.010

Date:

29-Apr-05 Release date: 16-Aug-05

Protein chain

P06746  (DPOLB_HUMAN) -  DNA polymerase beta from Homo sapiens

Seq: 335 a.a.

Struc: 325 a.a.

DNA/RNA chains

C-C-G-A-C-C-A-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

DOI no: 10.1016/j.str.2005.05.010

Structure (Camb) 13:1225-1233 (2005)

PubMed id: 16084394

Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate.

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

ABSTRACT

DNA polymerases occasionally insert the wrong nucleotide. For this error to become a mutation, the mispair must be extended. We report a structure of DNA polymerase beta (pol beta) with a DNA mismatch at the boundary of the polymerase active site. The structure of this complex indicates that the templating adenine of the mispair stacks with the primer terminus adenine while the templating (coding) cytosine is flipped out of the DNA helix. Soaking the crystals of the binary complex with dGTP resulted in crystals of a ternary substrate complex. In this case, the templating cytosine is observed within the DNA helix and forms Watson-Crick hydrogen bonds with the incoming dGTP. The adenine at the primer terminus has rotated into a syn-conformation to interact with the opposite adenine in a planar configuration. Yet, the 3'-hydroxyl on the primer terminus is out of position for efficient nucleotide insertion.

Selected figure(s)

Figure 4.
Figure 4. Structural Comparison of the Binary DNA and Ternary Substrate Complexes of DNA Polymerase b with an A-A Mismatch at the Boundary of the Active Site
A comparison of the polymerase and DNA conformations near the polymerase active site in the crystallographic structures of the binary (blue) and ternary (green) complexes with an A-A mismatch (yellow) at the primer terminus. As with matched termini, the N subdomain is observed to be open in the binary complex and closed in the ternary complex. Three striking conformational changes in the DNA are observed in forming the closed ternary substrate complex: (1) the adenine at the primer terminus rotates into a syn-conformation; (2) this permits the templating adenine of the mismatch to reposition itself opposite the primer terminus (n -1); (3) the coding template cytosine (orange) flips into the DNA helix, thereby forming Watson-Crick hydrogen bonds with the incoming dGTP (orange).

The above figure is reprinted by permission from Cell Press: Structure (Camb) (2005, 13, 1225-1233) copyright 2005.

Figure was selected by the author.