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PDBsum entry 4gx9

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protein Protein-protein interface(s) links
Transferase PDB id
4gx9
Jmol
Contents
Protein chains
312 a.a.
Waters ×277
PDB id:
4gx9
Name: Transferase
Title: Crystal structure of a DNA polymerase iii alpha-epsilon chim
Structure: DNA polymerase iii subunit epsilon, DNA polymeras subunit alpha. Chain: a, b, c, d. Fragment: poliii epsilon c-terminal domain (unp residues 20 poliii alpha php domain (unp residues 1-270). Engineered: yes. Mutation: yes
Source: Escherichia coli, synthetic, escherich organism_taxid: 83333, 32630, 83333. Strain: k12, k12. Gene: b0215, dnae, dnaq, jw0205, mutd, b0184, jw0179, polc. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.15Å     R-factor:   0.229     R-free:   0.291
Authors: N.Li,N.Horan,Z.-Q.Xu,D.Jacques,N.E.Dixon,A.J.Oakley
Key ref: K.Ozawa et al. (2013). Proofreading exonuclease on a tether: the complex between the E. coli DNA polymerase III subunits α, epsilon, θ and β reveals a highly flexible arrangement of the proofreading domain. Nucleic Acids Res, 41, 5354-5367. PubMed id: 23580545 DOI: 10.1093/nar/gkt162
Date:
04-Sep-12     Release date:   03-Apr-13    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P03007  (DPO3E_ECOLI) -  DNA polymerase III subunit epsilon
Seq:
Struc:
 
Seq:
Struc:
243 a.a.
312 a.a.
Protein chains
Pfam   ArchSchema ?
P10443  (DPO3A_ECOLI) -  DNA polymerase III subunit alpha
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1160 a.a.
312 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.7  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Deoxynucleoside triphosphate
+ DNA(n)
= diphosphate
+ DNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA replication   1 term 
  Biochemical function     catalytic activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1093/nar/gkt162 Nucleic Acids Res 41:5354-5367 (2013)
PubMed id: 23580545  
 
 
Proofreading exonuclease on a tether: the complex between the E. coli DNA polymerase III subunits α, epsilon, θ and β reveals a highly flexible arrangement of the proofreading domain.
K.Ozawa, N.P.Horan, A.Robinson, H.Yagi, F.R.Hill, S.Jergic, Z.Q.Xu, K.V.Loscha, N.Li, M.Tehei, A.J.Oakley, G.Otting, T.Huber, N.E.Dixon.
 
  ABSTRACT  
 
A complex of the three (αεθ) core subunits and the β2 sliding clamp is responsible for DNA synthesis by Pol III, the Escherichia coli chromosomal DNA replicase. The 1.7 Å crystal structure of a complex between the PHP domain of α (polymerase) and the C-terminal segment of ε (proofreading exonuclease) subunits shows that ε is attached to α at a site far from the polymerase active site. Both α and ε contain clamp-binding motifs (CBMs) that interact simultaneously with β2 in the polymerization mode of DNA replication by Pol III. Strengthening of both CBMs enables isolation of stable αεθ:β2 complexes. Nuclear magnetic resonance experiments with reconstituted αεθ:β2 demonstrate retention of high mobility of a segment of 22 residues in the linker that connects the exonuclease domain of ε with its α-binding segment. In spite of this, small-angle X-ray scattering data show that the isolated complex with strengthened CBMs has a compact, but still flexible, structure. Photo-crosslinking with p-benzoyl-L-phenylalanine incorporated at different sites in the α-PHP domain confirm the conformational variability of the tether. Structural models of the αεθ:β2 replicase complex with primer-template DNA combine all available structural data.