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PDBsum entry 1iqp

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protein ligands Protein-protein interface(s) links
Replication PDB id
1iqp
Jmol
Contents
Protein chains
(+ 0 more) 326 a.a. *
Ligands
ADP ×4
Waters ×244
* Residue conservation analysis
PDB id:
1iqp
Name: Replication
Title: Crystal structure of the clamp loader small subunit from pyrococcus furiosus
Structure: Rfcs. Chain: a, b, c, d, e, f. Synonym: replication factor c small subunit precursor. Engineered: yes
Source: Pyrococcus furiosus. Organism_taxid: 2261. Gene: rfcs. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Hexamer (from PQS)
Resolution:
2.80Å     R-factor:   0.224     R-free:   0.277
Authors: T.Oyama,Y.Ishino,I.K.O.Cann,S.Ishino,K.Morikawa
Key ref:
T.Oyama et al. (2001). Atomic structure of the clamp loader small subunit from Pyrococcus furiosus. Mol Cell, 8, 455-463. PubMed id: 11545747 DOI: 10.1016/S1097-2765(01)00328-8
Date:
24-Jul-01     Release date:   19-Sep-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8U4J3  (RFCS_PYRFU) -  Replication factor C small subunit
Seq:
Struc:
 
Seq:
Struc:
852 a.a.
326 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 47 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     DNA replication factor C complex   1 term 
  Biological process     DNA replication   1 term 
  Biochemical function     DNA binding     3 terms  

 

 
DOI no: 10.1016/S1097-2765(01)00328-8 Mol Cell 8:455-463 (2001)
PubMed id: 11545747  
 
 
Atomic structure of the clamp loader small subunit from Pyrococcus furiosus.
T.Oyama, Y.Ishino, I.K.Cann, S.Ishino, K.Morikawa.
 
  ABSTRACT  
 
In eukaryotic DNA replication, replication factor-C (RFC) acts as the clamp loader, which correctly installs the sliding clamp onto DNA strands at replication forks. The eukaryotic RFC is a complex consisting of one large and four small subunits. We have determined the crystal structure of the clamp loader small subunit (RFCS) from Pyrococcus furiosus. The six subunits, of which four bind ADP in their canonical nucleotide binding clefts, assemble into a dimer of semicircular trimers. The crescent-like architecture of each subunit formed by the three domains resembles that of the delta' subunit of the E. coli clamp loader. The trimeric architecture of archaeal RFCS, with its mobile N-terminal domains, involves intersubunit interactions that may be conserved in eukaryotic functional complexes.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Crystal Structure of P. furiosus RFCS(A) The overall fold of an RFCS subunit is shown by a ribbon representation. α helices and β strands are drawn by coils and arrows, respectively. The chain is colored cyan for Domain 1, green for Domain 2, and yellow for Domain 3. Walker A and B motifs are colored red. ADP is shown as a purple stick model.(B) The RFCS hexamer in the crystal is shown as a ribbon diagram viewed from the N-terminal side. The six subunits are colored blue, magenta, cyan, green, orange, and yellow-green for MolA to MolF, respectively. The four ADP molecules bound to MolA, MolB, MolC, and MolE are shown as red stick models.(C) A stereo view of an omit F[o]-F[c] electron density map contoured at 3 σ (ρ), drawn with ADP. Amino acid residues interacting with ADP are depicted. Water molecules are indicated by white spheres.(D) Orthogonal views of electrostatic potential mapped onto the molecular surfaces as calculated by the program GRASP (Nicholls and Honig, 1991). Positively charged surfaces are colored blue, and negatively charged surfaces are red. The figure in the upper left panel is viewed from the N-terminal side, as in (B). Trimer 1 (MolA to MolC) is indicated by a dotted line in the upper left (N-terminal side) and upper right (C-terminal side) panels
Figure 3.
Figure 3. Structure of RFCS Hexamers(A) Comparison of a hypothetical hexameric ring of RFCS (center) with the electron microscopic image (left). The 6-fold symmetry ring model was built from a semicircular trimer of RFCS in the crystal (right) and is drawn in top (upper) and side views (lower). One subunit in each hexamer is encircled. The EM 3D reconstructed images were obtained by essentially the same procedure as in our previous study (Mayanagi et al., 2001; K. Mayanagi and T. Miyata, personal communication). The scale bar indicated for the EM images is 50 Å.(B) Interaction scheme between subunits within the semicircular trimers, represented by an open-book view. Subunits with interfaces near the convex side of the crescent-shaped molecules are designated as “front,” while those with interfaces at the inner concave region of the crescents are designated as “back.” Only MolA and MolB are drawn as representative subunits. Segments contributing to the interfaces are colored blue for the front subunit and magenta for the back. In the front subunit, four segments, residues 4–14, 206–210, 229–231, and 262–271, contribute to Interface I (upper half), while two segments, residues 249–255 and 300–323, form Interface II (lower half). In the back subunit, residues 36–47 and 149–168 are involved in Interface I and residues 277–309 in Interface II. Intersubunit hydrogen bonding and hydrophobic interactions, which are observed in more than two interfaces of the total four, are indicated by red and green lines, respectively
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2001, 8, 455-463) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20532250 N.Chia, I.Cann, and G.J.Olsen (2010).
Evolution of DNA replication protein complexes in eukaryotes and Archaea.
  PLoS One, 5, e10866.  
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
19717601 Y.H.Chen, Y.Lin, A.Yoshinaga, B.Chhotani, J.L.Lorenzini, A.A.Crofts, S.Mei, R.I.Mackie, Y.Ishino, and I.K.Cann (2009).
Molecular analyses of a three-subunit euryarchaeal clamp loader complex from Methanosarcina acetivorans.
  J Bacteriol, 191, 6539-6549.  
18550799 L.Zhu, J.O.Wrabl, A.P.Hayashi, L.S.Rose, and P.J.Thomas (2008).
The torsin-family AAA+ protein OOC-5 contains a critical disulfide adjacent to Sensor-II that couples redox state to nucleotide binding.
  Mol Biol Cell, 19, 3599-3612.  
17493121 K.Imamura, K.Fukunaga, Y.Kawarabayasi, and Y.Ishino (2007).
Specific interactions of three proliferating cell nuclear antigens with replication-related proteins in Aeropyrum pernix.
  Mol Microbiol, 64, 308-318.  
17496095 K.Tori, M.Kimizu, S.Ishino, and Y.Ishino (2007).
DNA polymerases BI and D from the hyperthermophilic archaeon Pyrococcus furiosus both bind to proliferating cell nuclear antigen with their C-terminal PIP-box motifs.
  J Bacteriol, 189, 5652-5657.  
17501915 P.Guo, and T.J.Lee (2007).
Viral nanomotors for packaging of dsDNA and dsRNA.
  Mol Microbiol, 64, 886-903.  
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.  
16766187 A.F.Neuwald (2006).
Bayesian shadows of molecular mechanisms cast in the light of evolution.
  Trends Biochem Sci, 31, 374-382.  
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.  
17158702 E.R.Barry, and S.D.Bell (2006).
DNA replication in the archaea.
  Microbiol Mol Biol Rev, 70, 876-887.  
16608854 N.Y.Yao, A.Johnson, G.D.Bowman, J.Kuriyan, and M.O'Donnell (2006).
Mechanism of proliferating cell nuclear antigen clamp opening by replication factor C.
  J Biol Chem, 281, 17528-17539.  
16082778 A.F.Neuwald (2005).
Evolutionary clues to eukaryotic DNA clamp-loading mechanisms: analysis of the functional constraints imposed on replication factor C AAA+ ATPases.
  Nucleic Acids Res, 33, 3614-3628.  
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.  
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.  
16257971 Y.H.Chen, S.A.Kocherginskaya, Y.Lin, B.Sriratana, A.M.Lagunas, J.B.Robbins, R.I.Mackie, and I.K.Cann (2005).
Biochemical and mutational analyses of a unique clamp loader complex in the archaeon Methanosarcina acetivorans.
  J Biol Chem, 280, 41852-41863.  
14757052 A.Haroniti, C.Anderson, Z.Doddridge, L.Gardiner, C.J.Roberts, S.Allen, and P.Soultanas (2004).
The clamp-loader-helicase interaction in Bacillus. Atomic force microscopy reveals the structural organisation of the DnaB-tau complex in Bacillus.
  J Mol Biol, 336, 381-393.  
15201901 G.D.Bowman, M.O'Donnell, and J.Kuriyan (2004).
Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex.
  Nature, 429, 724-730.
PDB code: 1sxj
14717711 J.M.Gulbis, S.L.Kazmirski, J.Finkelstein, Z.Kelman, M.O'Donnell, and J.Kuriyan (2004).
Crystal structure of the chi:psi sub-assembly of the Escherichia coli DNA polymerase clamp-loader complex.
  Eur J Biochem, 271, 439-449.
PDB code: 1em8
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.  
15556993 S.L.Kazmirski, M.Podobnik, T.F.Weitze, M.O'Donnell, and J.Kuriyan (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.
PDB codes: 1xxh 1xxi
15208692 T.Miyata, T.Oyama, K.Mayanagi, S.Ishino, Y.Ishino, and K.Morikawa (2004).
The clamp-loading complex for processive DNA replication.
  Nat Struct Mol Biol, 11, 632-636.  
14527289 B.Grabowski, and Z.Kelman (2003).
Archeal DNA replication: eukaryal proteins in a bacterial context.
  Annu Rev Microbiol, 57, 487-516.  
12649440 S.Matsumiya, S.Ishino, Y.Ishino, and K.Morikawa (2003).
Intermolecular ion pairs maintain the toroidal structure of Pyrococcus furiosus PCNA.
  Protein Sci, 12, 823-831.
PDB codes: 1iz4 1iz5
12384579 A.Seybert, D.J.Scott, S.Scaife, M.R.Singleton, and D.B.Wigley (2002).
Biochemical characterisation of the clamp/clamp loader proteins from the euryarchaeon Archaeoglobus fulgidus.
  Nucleic Acids Res, 30, 4329-4338.  
12237462 C.Venclovas, M.E.Colvin, and M.P.Thelen (2002).
Molecular modeling-based analysis of interactions in the RFC-dependent clamp-loading process.
  Protein Sci, 11, 2403-2416.  
11959500 D.Jeruzalmi, M.O'Donnell, and J.Kuriyan (2002).
Clamp loaders and sliding clamps.
  Curr Opin Struct Biol, 12, 217-224.  
11927597 H.Yang, J.H.Chiang, S.Fitz-Gibbon, M.Lebel, A.A.Sartori, J.Jiricny, M.M.Slupska, and J.H.Miller (2002).
Direct interaction between uracil-DNA glycosylase and a proliferating cell nuclear antigen homolog in the crenarchaeon Pyrobaculum aerophilum.
  J Biol Chem, 277, 22271-22278.  
11856841 I.Lee, N.K.Lokanath, K.Min, S.C.Ha, D.Y.Kim, and K.K.Kim (2002).
Cloning, purification, crystallization and preliminary X-ray studies of RFC boxes II-VIII of replication factor C from Methanococcus jannaschii.
  Acta Crystallogr D Biol Crystallogr, 58, 519-521.  
11907025 J.D.Griffith, L.A.Lindsey-Boltz, and A.Sancar (2002).
Structures of the human Rad17-replication factor C and checkpoint Rad 9-1-1 complexes visualized by glycerol spray/low voltage microscopy.
  J Biol Chem, 277, 15233-15236.  
12234917 J.P.Erzberger, M.M.Pirruccello, and J.M.Berger (2002).
The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation.
  EMBO J, 21, 4763-4773.
PDB code: 1l8q
11790738 K.Daimon, Y.Kawarabayasi, H.Kikuchi, Y.Sako, and Y.Ishino (2002).
Three proliferating cell nuclear antigen-like proteins found in the hyperthermophilic archaeon Aeropyrum pernix: interactions with the two DNA polymerases.
  J Bacteriol, 184, 687-694.  
12415300 M.J.Davey, D.Jeruzalmi, J.Kuriyan, and M.O'Donnell (2002).
Motors and switches: AAA+ machines within the replisome.
  Nat Rev Mol Cell Biol, 3, 826-835.  
12370190 M.M.Hingorani, and M.M.Coman (2002).
On the specificity of interaction between the Saccharomyces cerevisiae clamp loader replication factor C and primed DNA templates during DNA replication.
  J Biol Chem, 277, 47213-47224.  
12209147 P.Chène (2002).
ATPases as drug targets: learning from their structure.
  Nat Rev Drug Discov, 1, 665-673.  
12296822 S.Matsumiya, S.Ishino, Y.Ishino, and K.Morikawa (2002).
Physical interaction between proliferating cell nuclear antigen and replication factor C from Pyrococcus furiosus.
  Genes Cells, 7, 911-922.
PDB code: 1isq
11525729 D.Jeruzalmi, M.O'Donnell, and J.Kuriyan (2001).
Crystal structure of the processivity clamp loader gamma (gamma) complex of E. coli DNA polymerase III.
  Cell, 106, 429-441.
PDB code: 1jr3
11709164 M.A.Trakselis, and S.J.Benkovic (2001).
Intricacies in ATP-dependent clamp loading: variations across replication systems.
  Structure, 9, 999.  
11719243 M.O'Donnell, D.Jeruzalmi, and J.Kuriyan (2001).
Clamp loader structure predicts the architecture of DNA polymerase III holoenzyme and RFC.
  Curr Biol, 11, R935-R946.  
11572772 V.Ellison, and B.Stillman (2001).
Opening of the clamp: an intimate view of an ATP-driven biological machine.
  Cell, 106, 655-660.  
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.