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PDBsum entry 1njg
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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1njg

 

 

 

 

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Contents
Protein chains
240 a.a. *
Ligands
SO4 ×3
Metals
_ZN ×2
Waters ×130
* Residue conservation analysis
PDB id:
1njg
Name: Transferase
Title: Nucleotide-free form of an isolated e. Coli clamp loader gamma subunit
Structure: DNA polymerase iii subunit gamma. Chain: a, b. Fragment: n-terminal domains 1 and 2. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: dnax. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.20Å     R-factor:   0.238     R-free:   0.268
Authors: M.Podobnik,T.F.Weitze,M.O'Donnell,J.Kuriyan
Key ref:
M.Podobnik et al. (2003). Nucleotide-induced conformational changes in an isolated Escherichia coli DNA polymerase III clamp loader subunit. Structure, 11, 253-263. PubMed id: 12623013 DOI: 10.1016/S0969-2126(03)00027-3
Date:
30-Dec-02     Release date:   01-Apr-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P06710  (DPO3X_ECOLI) -  DNA polymerase III subunit tau from Escherichia coli (strain K12)
Seq:
Struc: 		 
Seq:
Struc: 		643 a.a.
240 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.7  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
DNA(n)
 + 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(03)00027-3 Structure 11:253-263 (2003)
PubMed id: 12623013  
 
 
Nucleotide-induced conformational changes in an isolated Escherichia coli DNA polymerase III clamp loader subunit.
M.Podobnik, T.F.Weitze, M.O'Donnell, J.Kuriyan.
 
  ABSTRACT  
 
Sliding clamps are loaded onto DNA by ATP-driven clamp loader complexes. The structure of the E. coli clamp loader in a nucleotide-free state has been determined previously. We now report crystal structures of a truncated form of the isolated gamma-ATPase subunit, gamma(1-243), of the E. coli clamp loader, in nucleotide-free and bound forms. The gamma subunit adopts a defined conformation when empty, in which the nucleotide binding site is blocked. The binding of either ATPgammaS or ADP, which are shown to bind with equal affinity to gamma(1-243), induces a change in the relative orientation of the two domains such that nucleotides can be accommodated. This change would break one of the gamma:gamma interfaces seen in the empty clamp loader complex, and may represent one step in the activation process.
 
  Selected figure(s)  
 
Figure 8.
Figure 8. Schematic Diagram of Potential Rearrangement in the Clamp Loader Complex upon Nucleotide BindingThis represents a hypothetical sequence of events based on structural and biochemical evidence of conformational changes presented here and in [9]. Only three subunits of the g complex are shown for clarity. Green: d'; red: g1; blue: g2. S1: sensor 1/switch 2 helix a7, containing the SRC motif; P: P loop; S2: sensor 2 helix a10. Close contacts between the subunits are marked by yellow circles. ATP is drawn bound to the g1 subunit (brown circles are for the base and sugar, and white are for the phosphate groups). Arginine from the conserved SRC motif is indicated on the S1 (sensor 1) helices.
 
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 253-263) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19703275 A.Y.Mulkidjanian, and M.Y.Galperin (2009).
On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth.
  Biol Direct, 4, 27.  
17680687 M.Brylinski, and J.Skolnick (2008).
What is the relationship between the global structures of apo and holo proteins?
  Proteins, 70, 363-377.  
18424802 S.Chen, M.M.Coman, M.Sakato, M.O'Donnell, and M.M.Hingorani (2008).
Conserved residues in the delta subunit help the E. coli clamp loader, gamma complex, target primer-template DNA for clamp assembly.
  Nucleic Acids Res, 36, 3274-3286.  
17716973 K.Siddiqui, and B.Stillman (2007).
ATP-dependent assembly of the human origin recognition complex.
  J Biol Chem, 282, 32370-32383.  
17012286 A.F.Neuwald (2006).
Hypothesis: bacterial clamp loader ATPase activation through DNA-dependent repositioning of the catalytic base and of a trans-acting catalytic threonine.
  Nucleic Acids Res, 34, 5280-5290.  
16628222 A.Seybert, M.R.Singleton, N.Cook, D.R.Hall, and D.B.Wigley (2006).
Communication between subunits within an archaeal clamp-loader complex.
  EMBO J, 25, 2209-2218.
PDB codes: 2chg 2chq 2chv
16955075 C.Indiani, and M.O'Donnell (2006).
The replication clamp-loading machine at work in the three domains of life.
  Nat Rev Mol Cell Biol, 7, 751-761.  
15952889 A.Johnson, and M.O'Donnell (2005).
Cellular DNA replicases: components and dynamics at the replication fork.
  Annu Rev Biochem, 74, 283-315.  
14610068 A.K.Snyder, C.R.Williams, A.Johnson, M.O'Donnell, and L.B.Bloom (2004).
Mechanism of loading the Escherichia coli DNA polymerase III sliding clamp: II. Uncoupling the beta and DNA binding activities of the gamma complex.
  J Biol Chem, 279, 4386-4393.  
14610067 C.R.Williams, A.K.Snyder, P.Kuzmic, M.O'Donnell, and L.B.Bloom (2004).
Mechanism of loading the Escherichia coli DNA polymerase III sliding clamp: I. Two distinct activities for individual ATP sites in the gamma complex.
  J Biol Chem, 279, 4376-4385.  
15093841 M.Karplus, and Y.Q.Gao (2004).
Biomolecular motors: the F1-ATPase paradigm.
  Curr Opin Struct Biol, 14, 250-259.  
15364574 M.Magdalena Coman, M.Jin, R.Ceapa, J.Finkelstein, M.O'Donnell, B.T.Chait, and M.M.Hingorani (2004).
Dual functions, clamp opening and primer-template recognition, define a key clamp loader subunit.
  J Mol Biol, 342, 1457-1469.  
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.

 

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