spacer
spacer

PDBsum entry 3e0d

Go to PDB code: 
protein dna_rna ligands metals Protein-protein interface(s) links
Transferase/DNA PDB id
3e0d
Jmol
Contents
Protein chains
1148 a.a. *
DNA/RNA
Ligands
DTP ×2
Metals
_CA ×2
* Residue conservation analysis
PDB id:
3e0d
Name: Transferase/DNA
Title: Insights into the replisome from the crystral structure of the ternary complex of the eubacterial DNA polymerase iii alpha-subunit
Structure: DNA substrate template strand. Chain: c, e. Engineered: yes. DNA substrate primer strand. Chain: d, f. Engineered: yes. DNA polymerase iii subunit alpha. Chain: a, b. Engineered: yes.
Source: Synthetic: yes. Thermus aquaticus. Organism_taxid: 271. Gene: dnae. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
4.60Å     R-factor:   0.287     R-free:   0.271
Authors: R.A.Wing,S.Bailey,T.A.Steitz
Key ref:
R.A.Wing et al. (2008). Insights into the replisome from the structure of a ternary complex of the DNA polymerase III alpha-subunit. J Mol Biol, 382, 859-869. PubMed id: 18691598 DOI: 10.1016/j.jmb.2008.07.058
Date:
31-Jul-08     Release date:   23-Sep-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9XDH5  (DPO3A_THEAQ) -  DNA polymerase III subunit alpha
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1220 a.a.
1148 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 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
Bound ligand (Het Group name = DTP)
matches with 64.00% similarity
+ 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!
  Cellular component     cytoplasm   1 term 
  Biological process     DNA biosynthetic process   3 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2008.07.058 J Mol Biol 382:859-869 (2008)
PubMed id: 18691598  
 
 
Insights into the replisome from the structure of a ternary complex of the DNA polymerase III alpha-subunit.
R.A.Wing, S.Bailey, T.A.Steitz.
 
  ABSTRACT  
 
The crystal structure of the catalytic alpha-subunit of the DNA polymerase III (Pol IIIalpha) holoenzyme bound to primer-template DNA and an incoming deoxy-nucleoside 5'-triphosphate has been determined at 4.6-A resolution. The polymerase interacts with the sugar-phosphate backbone of the DNA across its minor groove, which is made possible by significant movements of the thumb, finger, and beta-binding domains relative to their orientations in the unliganded polymerase structure. Additionally, the DNA and incoming nucleotide are bound to the active site of Pol IIIalpha nearly identically as they are in their complex with DNA polymerase beta, thereby proving that the eubacterial replicating polymerase, but not the eukaryotic replicating polymerase, is homologous to DNA polymerase beta. Finally, superimposing a recent structure of the clamp bound to DNA on this Pol IIIalpha complex with DNA places a loop of the beta-binding domain into the appropriate clamp cleft and supports a mechanism of polymerase switching.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Crystal structure of a replicating complex of T. aquaticus PolIIIα. (a) A view of the crystal structure of the replicating complex of T. aquaticus PolIIIα. Domains are labeled as follows: PHP nuclease, yellow; palm, pink; thumb, light green; index finger, light blue; middle finger, dark blue; β-binding, orange; and CTD, red. The template and primer strands are represented as spheres and shown in wheat and white, respectively. The primer-terminal 3′ base is depicted with blue spheres, and the incoming nucleotide is depicted with red spheres. PolIIIα is depicted in a cartoon representation. The density for the downstream DNA template strand is represented in mesh. (b) Close-up of the active site of PolIIIα. PolIIIα is depicted using a surface representation. The DNA substrate is depicted as sticks and shown as in the left panel. The incoming nucleotide and primer-terminal 3′ base are shown in red and blue, respectively. Key active-site residues are labeled as follows: D463, D465, and D618 are shown in red; K616 is in yellow; S426 is in green; and R767 is in blue. The active-site helix is shown in magenta.
Figure 3.
Fig. 3. Interactions with the DNA substrate. (a) Surface representation of interactions between the thumb domain of PolIIIα and the DNA substrate in a cartoon representation. Green surfaces indicate the thumb domain, with blue surfaces representing residues proposed to interact with the DNA substrate. Yellow surfaces represent the PHP nuclease domain. The polymerase active site is seen on the left as demarcated by the blue stick representation of the primer-terminal 3′ base (ddC) and the red stick representation of the incoming nucleotide (dATP). (b) Surface representation of interactions between the β-binding domain of PolIIIα and the DNA substrate in a cartoon representation. Orange surfaces indicate the β-binding domain with three key loops implicated in DNA binding labeled as follows: Taq927–Taq923, blue; HhH motif Taq892–Taq910, cyan; and Taq846–Taq852, purple. Positively charged residues that are within proximity to interact with the sugar–phosphate backbone are labeled, and their positions are indicated with white arrows. An additional arrow points to the location of the polymerase active site. (c) The observed DNA substrate of PolIIIα is depicted using a cartoon representation with the primer strand shown in white and the template strand shown in wheat. Idealized B-form DNA aligned with the DNA substrate prior to bending is displayed in a surface representation. Black lines indicate the helical axes of the DNA substrate (outside of the active site) and the idealized B-form DNA. The primer-terminal 3′ base is represented in blue sticks. The loops of the thumb domain (Taq492–Taq499 and Taq569–Taq575) that induce DNA bending are shown in green and represented as a surface.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 382, 859-869) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20123134 J.D.Pata (2010).
Structural diversity of the Y-family DNA polymerases.
  Biochim Biophys Acta, 1804, 1124-1135.  
19173290 M.J.McCauley, and M.C.Williams (2009).
Optical tweezers experiments resolve distinct modes of DNA-protein binding.
  Biopolymers, 91, 265-282.  
19696739 R.E.Georgescu, I.Kurth, N.Y.Yao, J.Stewart, O.Yurieva, and M.O'Donnell (2009).
Mechanism of polymerase collision release from sliding clamps on the lagging strand.
  EMBO J, 28, 2981-2991.  
19106294 M.H.Lamers, and M.O'Donnell (2008).
A consensus view of DNA binding by the C family of replicative DNA polymerases.
  Proc Natl Acad Sci U S A, 105, 20565-20566.  
19106298 R.J.Evans, D.R.Davies, J.M.Bullard, J.Christensen, L.S.Green, J.W.Guiles, J.D.Pata, W.K.Ribble, N.Janjic, and T.C.Jarvis (2008).
Structure of PolC reveals unique DNA binding and fidelity determinants.
  Proc Natl Acad Sci U S A, 105, 20695-20700.
PDB codes: 3f2b 3f2c 3f2d
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.