PDBsum entry 1j53

Transferase

PDB id: 1j53

Contents

Protein chain

174 a.a. *

Ligands

TMP ×2

EDO ×2

Metals

_MN ×2

Waters ×229

* Residue conservation analysis

PDB id:

1j53

Name:

Transferase

Title:

Structure of the n-terminal exonuclease domain of the epsilon subunit of e.Coli DNA polymerase iii at ph 8.5

Structure:

DNA polymerase iii, epsilon chain. Chain: a. Fragment: n-terminal exonuclease domain (residues 1-186). Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: enterobacteria phage t7. Expression_system_taxid: 10760.

Resolution:

1.80Å R-factor: 0.199 R-free: 0.227

Authors:

S.Hamdan,P.D.Carr,S.E.Brown,D.L.Ollis,N.E.Dixon

Key ref:

S.Hamdan et al. (2002). Structural basis for proofreading during replication of the Escherichia coli chromosome. Structure, 10, 535-546. PubMed id: 11937058 DOI: 10.1016/S0969-2126(02)00738-4

Date:

22-Jan-02 Release date: 16-Oct-02

Protein chain

P03007  (DPO3E_ECOLI) -  DNA polymerase III subunit epsilon from Escherichia coli (strain K12)

Seq: 243 a.a.

Struc: 174 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

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

Added reference

DOI no: 10.1016/S0969-2126(02)00738-4

Structure 10:535-546 (2002)

PubMed id: 11937058

Structural basis for proofreading during replication of the Escherichia coli chromosome.

S.Hamdan, P.D.Carr, S.E.Brown, D.L.Ollis, N.E.Dixon.

ABSTRACT

The epsilon subunit of the Escherichia coli replicative DNA polymerase III is the proofreading 3'-5' exonuclease. Structures of its catalytic N-terminal domain (epsilon186) were determined at two pH values (5.8 and 8.5) at resolutions of 1.7-1.8 A, in complex with two Mn(II) ions and a nucleotide product of its reaction, thymidine 5'-monophosphate. The protein structure is built around a core five-stranded beta sheet that is a common feature of members of the DnaQ superfamily. The structures were identical, except for differences in the way TMP and water molecules are coordinated to the binuclear metal center in the active site. These data are used to develop a mechanism for epsilon and to produce a plausible model of the complex of epsilon186 with DNA.

Selected figure(s)

Figure 3.
Figure 3. Structures of the Active Sites of epsilon, Greek 186 and Other Exonuclease Domains(A and B) Low- and high-pH structures, respectively, of the active site of epsilon, Greek 186. The two Mn(II) ions, Mn[A] and Mn[B] are shown (in orange) coordinated to the 5'-phosphate of TMP. The remainder of the TMP molecules are omitted for clarity (but see Figure 4). Coordinated-water molecules are represented by red spheres.(C-E) Comparative structures of the 3'-5' exonuclease active sites of exonuclease I (PDB code 1FXX) [41], DNA polymerase I (1KRP) [51], and bacteriophage T4 DNA polymerase (1NOY) [7]. Structures were aligned as in Figure 2, and diagrams were drawn using RIBBONS [78].

The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 535-546) copyright 2002.

Figure was selected by the author.