PDBsum entry 2hpm

Transferase

PDB id: 2hpm

Contents

Protein chain

1143 a.a. *

Ligands

3PO

Metals

_ZN ×2

_MG ×2

_CL ×2

* Residue conservation analysis

PDB id:

2hpm

Name:

Transferase

Title:

Eubacterial and eukaryotic replicative DNA polymerases are not homologous: x-ray structure of DNA polymerase iii

Structure:

DNA polymerase iii alpha subunit. Chain: a. Engineered: yes

Source:

Thermus aquaticus. Organism_taxid: 271. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.70Å R-factor: 0.243 R-free: 0.311

Authors:

S.Bailey,R.A.Wing,T.A.Steitz

Key ref:

S.Bailey et al. (2006). The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases. Cell, 126, 893-904. PubMed id: 16959569 DOI: 10.1016/j.cell.2006.07.027

Date:

17-Jul-06 Release date: 19-Sep-06

Protein chain

Q9XDH5  (DPO3A_THEAQ) -  DNA polymerase III subunit alpha from Thermus aquaticus

Seq: 1220 a.a.

Struc: 1143 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

DNA(n) + 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) (Bound ligand (Het Group name = 3PO) matches with 69.23% similarity) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.cell.2006.07.027

Cell 126:893-904 (2006)

PubMed id: 16959569

The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases.

S.Bailey, R.A.Wing, T.A.Steitz.

ABSTRACT

The crystal structure of Thermus aquaticus DNA polymerase III alpha subunit reveals that the structure of the catalytic domain of the eubacterial replicative polymerase is unrelated to that of the eukaryotic replicative polymerase but rather belongs to the Polbeta-like nucleotidyltransferase superfamily. A model of the polymerase complexed with both DNA and beta-sliding clamp interacting with a reoriented binding domain and internal beta binding site was constructed that is consistent with existing biochemical data. Within the crystal, two C-terminal domains are interacting through a surface that is larger than many dimer interfaces. Since replicative polymerases of eubacteria and eukaryotes/archaea are not homologous, the nature of the replicative polymerase in the last common ancestor is unknown. Although other possibilities have been proposed, the plausibility of a ribozyme DNA polymerase should be considered.

Selected figure(s)

Figure 1.
Figure 1. A Representative Region of Electron Density
Unbiased F[o] − F[c] electron density map contoured at 3σ. The residues, which are represented as sticks, were omitted from the map calculation.

Figure 2.
Figure 2. Crystal Structure of Taq DNA Polymerase III α Subunit
(Top middle) A schematic diagram of the domain positions in the PolIIIα sequence. The domains are labeled and colored as follows: the PHP domain in yellow, the palm in magenta, the thumb in green, the fingers in light blue, the β binding domain in orange, and the CTD in red. (Center) Two orthogonal views of the surface of PolIIIα colored as in the schematic above. Ribbon diagrams of the individual domains are shown around the outside.

The above figures are reprinted by permission from Cell Press: Cell (2006, 126, 893-904) copyright 2006.

Figures were selected by an automated process.