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

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
338 a.a. *
(+ 0 more) 364 a.a. *
334 a.a. *
Ligands
AGS ×4
PO4 ×2
Metals
_ZN ×8
* Residue conservation analysis
PDB id:
1xxh
Name: Transferase
Title: Atpgs bound e. Coli clamp loader complex
Structure: DNA polymerase iii, delta subunit. Chain: a, f. Engineered: yes. DNA polymerase iii subunit gamma. Chain: b, c, d, g, h, i. Engineered: yes. DNA polymerase iii, delta prime subunit. Chain: e, j. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: hola. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: dnax, dnaz, dnazx. Gene: holb. Expression_system_taxid: 562
Biol. unit: Pentamer (from PQS)
Resolution:
3.45Å     R-factor:   0.315     R-free:   0.350
Authors: S.L.Kazmirski,M.Podobnik,T.F.Weitze,M.O'Donnell,J.Kuriyan
Key ref:
S.L.Kazmirski et al. (2004). Structural analysis of the inactive state of the Escherichia coli DNA polymerase clamp-loader complex. Proc Natl Acad Sci U S A, 101, 16750-16755. PubMed id: 15556993 DOI: 10.1073/pnas.0407904101
Date:
05-Nov-04     Release date:   07-Dec-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P28630  (HOLA_ECOLI) -  DNA polymerase III subunit delta from Escherichia coli (strain K12)
Seq:
Struc: 		343 a.a.
338 a.a.
Protein chains
Pfam   ArchSchema ?
P06710  (DPO3X_ECOLI) -  DNA polymerase III subunit tau from Escherichia coli (strain K12)
Seq:
Struc: 		 
Seq:
Struc: 		643 a.a.
364 a.a.
Protein chains
Pfam   ArchSchema ?
P28631  (HOLB_ECOLI) -  DNA polymerase III subunit delta' from Escherichia coli (strain K12)
Seq:
Struc: 		334 a.a.
334 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H, I, J: 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)
Bound ligand (Het Group name = PO4)
matches with 55.56% similarity 		+ diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1073/pnas.0407904101 Proc Natl Acad Sci U S A 101:16750-16755 (2004)
PubMed id: 15556993  
 
 
Structural analysis of the inactive state of the Escherichia coli DNA polymerase clamp-loader complex.
S.L.Kazmirski, M.Podobnik, T.F.Weitze, M.O'Donnell, J.Kuriyan.
 
  ABSTRACT  
 
Clamp-loader complexes are heteropentameric AAA+ ATPases that load sliding clamps onto DNA. The structure of the nucleotide-free Escherichia coli clamp loader had been determined previously and led to the proposal that the clamp-loader cycles between an inactive state, in which the ATPase domains form a closed ring, and an active state that opens up to form a "C" shape. The crystal structure was interpreted as being closer to the active state than the inactive state. The crystal structure of a nucleotide-bound eukaryotic clamp loader [replication factor C (RFC)] revealed a different and more tightly packed spiral organization of the ATPase domains, raising questions about the significance of the conformation seen earlier for the bacterial clamp loader. We describe crystal structures of the E. coli clamp-loader complex bound to the ATP analog ATPgammaS (at a resolution of 3.5 A) and ADP (at a resolution of 4.1 A). These structures are similar to that of the nucleotide-free clamp-loader complex. Only two of the three functional ATP-binding sites are occupied by ATPgammaS or ADP in these structures, and the bound nucleotides make no interfacial contacts in the complex. These results, along with data from isothermal titration calorimetry, molecular dynamics simulations, and comparison with the RFC structure, suggest that the more open form of the E. coli clamp loader described earlier and in the present work corresponds to a stable inactive state of the clamp loader in which the ATPase domains are prevented from engaging the clamp in the highly cooperative manner seen in the fully ATP-loaded RFC-clamp structure.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Structure of the clamp-loader complex. (A) Two views of the structure of the ATP S complex. The A subunit is , which is primarily responsible for opening the clamp. The ATP-binding subunits, , are labeled B-D. The E subunit is '. (B) Schematic diagram showing a suggested mechanism for clamp binding by the clamp-loader complex. Illustrations of protein structures were generated by using PYMOL (43). 		Figure 3.
Fig. 3. ITC binding curves for the clamp-loader complex in combination with various nucleotides.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20543826 N.Jiménez-Menéndez, P.Fernández-Millán, A.Rubio-Cosials, C.Arnan, J.Montoya, H.T.Jacobs, P.Bernadó, M.Coll, I.Usón, and M.Solà (2010).
Human mitochondrial mTERF wraps around DNA through a left-handed superhelical tandem repeat.
  Nat Struct Mol Biol, 17, 891-893.
PDB codes: 3n6s 3n7q
20162627 O.Doppelt-Azeroual, F.Delfaud, F.Moriaud, and A.G.de Brevern (2010).
Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins.
  Protein Sci, 19, 847-867.  
20113510 R.McNally, G.D.Bowman, E.R.Goedken, M.O'Donnell, and J.Kuriyan (2010).
Analysis of the role of PCNA-DNA contacts during clamp loading.
  BMC Struct Biol, 10, 3.
PDB code: 3k4x
20413500 R.Reyes-Lamothe, D.J.Sherratt, and M.C.Leake (2010).
Stoichiometry and architecture of active DNA replication machinery in Escherichia coli.
  Science, 328, 498-501.  
19576301 Z.Zhuang, and Y.Ai (2010).
Processivity factor of DNA polymerase and its expanding role in normal and translesion DNA synthesis.
  Biochim Biophys Acta, 1804, 1081-1093.  
19759003 J.A.Thompson, C.O.Paschall, M.O'Donnell, and L.B.Bloom (2009).
A slow ATP-induced conformational change limits the rate of DNA binding but not the rate of beta clamp binding by the escherichia coli gamma complex clamp loader.
  J Biol Chem, 284, 32147-32157.  
19450514 K.R.Simonetta, S.L.Kazmirski, E.R.Goedken, A.J.Cantor, B.A.Kelch, R.McNally, S.N.Seyedin, D.L.Makino, M.O'Donnell, and J.Kuriyan (2009).
The mechanism of ATP-dependent primer-template recognition by a clamp loader complex.
  Cell, 137, 659-671.
PDB codes: 3glf 3glg 3glh 3gli
19213612 L.B.Bloom (2009).
Loading clamps for DNA replication and repair.
  DNA Repair (Amst), 8, 570-578.  
19289466 P.A.Meyer, P.Ye, M.H.Suh, M.Zhang, and J.Fu (2009).
Structure of the 12-subunit RNA polymerase II refined with the aid of anomalous diffraction data.
  J Biol Chem, 284, 12933-12939.
PDB code: 3fki
17962021 A.F.Neuwald (2007).
The CHAIN program: forging evolutionary links to underlying mechanisms.
  Trends Biochem Sci, 32, 487-493.  
17452361 X.C.Su, S.Jergic, M.A.Keniry, N.E.Dixon, and G.Otting (2007).
Solution structure of Domains IVa and V of the tau subunit of Escherichia coli DNA polymerase III and interaction with the alpha subunit.
  Nucleic Acids Res, 35, 2825-2832.
PDB code: 2aya
16220545 A.Ababou, and J.E.Ladbury (2006).
Survey of the year 2004: literature on applications of isothermal titration calorimetry.
  J Mol Recognit, 19, 79-89.  
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.  
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.  
15698560 A.T.Brunger (2005).
Low-resolution crystallography is coming of age.
  Structure, 13, 171-172.  
15665871 E.R.Goedken, S.L.Kazmirski, G.D.Bowman, M.O'Donnell, and J.Kuriyan (2005).
Mapping the interaction of DNA with the Escherichia coli DNA polymerase clamp loader complex.
  Nat Struct Mol Biol, 12, 183-190.  
16169903 S.L.Kazmirski, Y.Zhao, G.D.Bowman, M.O'donnell, and J.Kuriyan (2005).
Out-of-plane motions in open sliding clamps: molecular dynamics simulations of eukaryotic and archaeal proliferating cell nuclear antigen.
  Proc Natl Acad Sci U S A, 102, 13801-13806.  
16169902 T.Miyata, H.Suzuki, T.Oyama, K.Mayanagi, Y.Ishino, and K.Morikawa (2005).
Open clamp structure in the clamp-loading complex visualized by electron microscopic image analysis.
  Proc Natl Acad Sci U S A, 102, 13795-13800.  
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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