PDBsum entry 2hnh

Transferase

PDB id: 2hnh

Contents

Protein chain

910 a.a. *

Ligands

PO4 ×3

Waters ×399

* Residue conservation analysis

PDB id:

2hnh

Name:

Transferase

Title:

Crystal structure of the catalytic alpha subunit of e. Coli replicative DNA polymerase iii

Structure:

DNA polymerase iii alpha subunit. Chain: a. Fragment: catalytic fragment (1-917). Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: dnae, polc. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Monomer (from PQS)

Resolution:

2.30Å R-factor: 0.190 R-free: 0.258

Authors:

M.H.Meindert,R.E.Georgescu,S.Lee,M.O'Donnell,J.Kuriyan

Key ref:

M.H.Lamers et al. (2006). Crystal structure of the catalytic alpha subunit of E. coli replicative DNA polymerase III. Cell, 126, 881-892. PubMed id: 16959568 DOI: 10.1016/j.cell.2006.07.028

Date:

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

Protein chain

P10443  (DPO3A_ECOLI) -  DNA polymerase III subunit alpha from Escherichia coli (strain K12)

Seq: 1160 a.a.

Struc: 910 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 = PO4) matches with 55.56% similarity) + diphosphate

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

Added reference

DOI no: 10.1016/j.cell.2006.07.028

Cell 126:881-892 (2006)

PubMed id: 16959568

Crystal structure of the catalytic alpha subunit of E. coli replicative DNA polymerase III.

M.H.Lamers, R.E.Georgescu, S.G.Lee, M.O'Donnell, J.Kuriyan.

ABSTRACT

Bacterial replicative DNA polymerases such as Polymerase III (Pol III) share no sequence similarity with other polymerases. The crystal structure, determined at 2.3 A resolution, of a large fragment of Pol III (residues 1-917), reveals a unique chain fold with localized similarity in the catalytic domain to DNA polymerase beta and related nucleotidyltransferases. The structure of Pol III is strikingly different from those of members of the canonical DNA polymerase families, which include eukaryotic replicative polymerases, suggesting that the DNA replication machinery in bacteria arose independently. A structural element near the active site in Pol III that is not present in nucleotidyltransferases but which resembles an element at the active sites of some canonical DNA polymerases suggests that, at a more distant level, all DNA polymerases may share a common ancestor. The structure also suggests a model for interaction of Pol III with the sliding clamp and DNA.

Selected figure(s)

Figure 1.
Figure 1. Overview of DNA Pol III Structure
(A) Top view in stereo and (B) side view in stereo. The location of the active site residues in the Palm domain are indicated by black spheres and the location of the phosphate ion in the PHP domain by red spheres. (C) The core region of Pol III alone resembles a cupped righthand shape. (PHP domain and ring and little Finger subdomains removed.)

Figure 4.
Figure 4. Pol III PHP Active Site Is Similar to that of DHH Phosphoesterases
(A) Surface representation showing PHP, Thumb, and Palm domains (similar view as in Figure 1B). A narrow groove runs from the Palm domain into a shallow cavity in the PHP domain that has phosphate bound. (B) Detailed view of shallow cavity in PHP domain is shown. (C) Active site of Streptococcus mutans PPase II (Merckel et al., 2001) is shown. Green sphere indicates a Mg^2+ ion and purple spheres Mn^2+ ions. The overall structure of this protein is unrelated to that of the PHP domain of Pol III.

The above figures are reprinted by permission from Cell Press: Cell (2006, 126, 881-892) copyright 2006.

Figures were selected by an automated process.