PDBsum entry 2ido

Transferase

PDB id: 2ido

Contents

Protein chains

173 a.a. *

75 a.a. *

Ligands

TMP ×2

EDO

Metals

_MN ×5

Waters ×429

* Residue conservation analysis

PDB id:

2ido

Name:

Transferase

Title:

Structure of the e. Coli pol iii epsilon-hot proofreading complex

Structure:

DNA polymerase iii epsilon subunit. Chain: a, c. Fragment: exonuclease domain. Engineered: yes. Hot protein. Chain: b, d. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: dnaq, mutd. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Enterobacteria phage. Organism_taxid: 10678. Strain: p1. Gene: hot.

Biol. unit:

Dimer (from PQS)

Resolution:

2.10Å R-factor: 0.206 R-free: 0.244

Authors:

T.W.Kirby,S.Harvey,E.F.Derose,S.Chalov,A.K.Chikova,F.W.Perrino, R.M.Schaaper,R.E.London,L.C.Pedersen

Key ref:

T.W.Kirby et al. (2006). Structure of the Escherichia coli DNA polymerase III epsilon-HOT proofreading complex. J Biol Chem, 281, 38466-38471. PubMed id: 16973612 DOI: 10.1074/jbc.M606917200

Date:

15-Sep-06 Release date: 14-Nov-06

Protein chains

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

Seq: 243 a.a.

Struc: 173 a.a.*

Protein chains

Q71T70  (Q71T70_BPP1) -  Hot from Escherichia phage P1

Seq: 87 a.a.

Struc: 75 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, C: 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: 10.1074/jbc.M606917200

J Biol Chem 281:38466-38471 (2006)

PubMed id: 16973612

Structure of the Escherichia coli DNA polymerase III epsilon-HOT proofreading complex.

T.W.Kirby, S.Harvey, E.F.DeRose, S.Chalov, A.K.Chikova, F.W.Perrino, R.M.Schaaper, R.E.London, L.C.Pedersen.

ABSTRACT

The epsilon subunit of Escherichia coli DNA polymerase III possesses 3'-exonucleolytic proofreading activity. Within the Pol III core, epsilon is tightly bound between the alpha subunit (DNA polymerase) and subunit. Here, we present the crystal structure of epsilon in complex with HOT, the bacteriophage P1-encoded homolog of , at 2.1 A resolution. The epsilon-HOT interface is defined by two areas of contact: an interaction of the previously unstructured N terminus of HOT with an edge of the epsilon central beta-sheet as well as interactions between HOT and the catalytically important helix alpha1-loop-helix alpha2 motif of epsilon. This structure provides insight into how HOT and, by implication, may stabilize the epsilon subunit, thus promoting efficient proofreading during chromosomal replication.

Selected figure(s)

Figure 2.
FIGURE 2. Variation in 186 crystallographic structures. A, superposition of the crystal structures of the two molecules of 186 in the asymmetric unit of the 186-HOT complex, molecule A (blue) and molecule C (red). B, superposition of the previously determined 186 (green) (Protein Data Bank code 1J54) with 186 molecule C (red) of the 186-HOT complex.

Figure 6.
FIGURE 6. Stereo view of mutator residues. Amino acids of that lead to a mutator phenotype when specifically substituted are shown in red on the structure of the 186-HOT complex. HOT is in orange, and 186 is in blue. Known mutator residues are Asp^12 (a), Glu^14 (b), Thr^15 (c), Thr^16 (d), Gly^17 (e), Arg^56 (f), His^66 (g), Val^96 (h), Asp^103 (i), His^162 (j), Ala^161 (k), Asp^167 (m), Leu^171 (n), and Gly^180 (o).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 38466-38471) copyright 2006.

Figures were selected by an automated process.