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PDBsum entry 2qby
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protein dna_rna ligands metals Protein-protein interface(s) links
Replication/DNA PDB id
2qby

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
366 a.a. *
368 a.a. *
DNA/RNA
Ligands
SPD ×2
ADP ×2
Metals
__K
_MG ×2
Waters ×4
* Residue conservation analysis
PDB id:
2qby
Name: Replication/DNA
Title: Crystal structure of a heterodimer of cdc6/orc1 initiators bound to origin DNA (from s. Solfataricus)
Structure: DNA (33-mer). Chain: c. Engineered: yes. DNA (33-mer). Chain: d. Engineered: yes. Cell division control protein 6 homolog 1. Chain: a. Fragment: residues 15-397.
Source: Synthetic: yes. Sulfolobus solfataricus. Organism_taxid: 2287. Gene: cdc6-1. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: cdc6-3.
Resolution:
3.35Å     R-factor:   0.226     R-free:   0.269
Authors: E.L.Cunningham Dueber,J.E.Corn,S.D.Bell,J.M.Berger
Key ref:
E.L.Dueber et al. (2007). Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex. Science, 317, 1210-1213. PubMed id: 17761879 DOI: 10.1126/science.1143690
Date:
18-Jun-07     Release date:   11-Sep-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q980N4  (CDC61_SULSO) -  ORC1-type DNA replication protein 1 from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Seq:
Struc: 		397 a.a.
366 a.a.
Protein chain
Pfam   ArchSchema ?
Q97WM8  (CDC63_SULSO) -  ORC1-type DNA replication protein 3 from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Seq:
Struc: 		394 a.a.
368 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  A-G-A-T-T-T-T-C-A-G-A-T-G-A-A-A-C-G-T-A-G-G-A-A-A-T-T-T-A-C-A-C-T 33 bases
  T-G-T-A-A-A-T-T-T-C-C-T-A-C-G-T-T-T-C-A-T-C-T-G-A-A-A-A-T-C-T-A-G 33 bases

 

 
DOI no: 10.1126/science.1143690 Science 317:1210-1213 (2007)
PubMed id: 17761879  
 
 
Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex.
E.L.Dueber, J.E.Corn, S.D.Bell, J.M.Berger.
 
  ABSTRACT  
 
The faithful duplication of genetic material depends on essential DNA replication initiation factors. Cellular initiators form higher-order assemblies on replication origins, using adenosine triphosphate (ATP) to locally remodel duplex DNA and facilitate proper loading of synthetic replisomal components. To better understand initiator function, we determined the 3.4 angstrom-resolution structure of an archaeal Cdc6/Orc1 heterodimer bound to origin DNA. The structure demonstrates that, in addition to conventional DNA binding elements, initiators use their AAA+ ATPase domains to recognize origin DNA. Together these interactions establish the polarity of initiator assembly on the origin and induce substantial distortions into origin DNA strands. Biochemical and comparative analyses indicate that AAA+/DNA contacts observed in the structure are dynamic and evolutionarily conserved, suggesting that the complex forms a core component of the basal initiation machinery.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Initiator/origin complex. (A) Schematic of oriC2, highlighting sequences recognized by Orc1-1, Orc1-2, and Orc1-3 paralogs (purple, gray, and teal arrows, respectively). The direction of the purple arrows reflects the 5'-to-3' convention of the mORB consensus sequence; the C2- and C3-site arrows indicate the relative orientations of these repeats. The dashed box denotes the C3/mORB dual site used in the cocrystal structure. DUE, DNA unwinding element. (B) A cartoon of Orc1-1 illustrates the relative orientation of the initiator's subdomains, with the ISM of the AAA+ domain in purple. ADP, black sticks; magnesium ions, magenta sphere. (C) Global architecture of the Orc1-1/Orc1-3 DNA complex. Protein, purple and teal; DNA, orange; ADP, blacksticks; magnesium ions, magenta spheres. (D) Electrostatic surface representations of Orc1-1 and Orc1-3. The yellow line demarcates the boundary between protomers. 		Figure 4.
Fig. 4. Initiator AAA+ interactions. (A) The AAA+ domains of ATP-bound DnaA (Aquifex aeolicas, Protein Data Bank accession number 2HCB) (24) assemble in a head-to-tail oligomer that places the arginine finger of the box VII helix (gold) into the ATPase active site of the adjacent protomer. (B) Stereo view of the Orc1-1/Orc1-3 DNA complex shows that contacts between adenosine diphosphate–bound initiators and DNA orient successive AAA+ domains into a similar, albeit more open, configuration to that of oligomerized DnaA. For clarity, only initiator AAA+ domains are shown in (A) and (B). Bound nucleotides (black) and magnesium ions (magenta) are shown as spheres.
 
  The above figures are reprinted by permission from the AAAs: Science (2007, 317, 1210-1213) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21227921 E.C.Dueber, A.Costa, J.E.Corn, S.D.Bell, and J.M.Berger (2011).
Molecular determinants of origin discrimination by Orc1 initiators in archaea.
  Nucleic Acids Res, 39, 3621-3631.  
21964332 K.E.Duderstadt, K.Chuang, and J.M.Berger (2011).
DNA stretching by bacterial initiators promotes replication origin opening.
  Nature, 478, 209-213.
PDB code: 3r8f
20680317 M.T.Hayashi, and H.Masukata (2011).
Regulation of DNA replication by chromatin structures: accessibility and recruitment.
  Chromosoma, 120, 39-46.  
20130679 H.Kawakami, and T.Katayama (2010).
DnaA, ORC, and Cdc6: similarity beyond the domains of life and diversity.
  Biochem Cell Biol, 88, 49-62.  
20335175 J.Jee, T.Mizuno, K.Kamada, H.Tochio, Y.Chiba, K.Yanagi, G.Yasuda, H.Hiroaki, F.Hanaoka, and M.Shirakawa (2010).
Structure and mutagenesis studies of the C-terminal region of licensing factor Cdt1 enable the identification of key residues for binding to replicative helicase Mcm proteins.
  J Biol Chem, 285, 15931-15940.
PDB code: 2rqq
19690980 J.Kusic, B.Tomic, A.Divac, and S.Kojic (2010).
Human initiation protein Orc4 prefers triple stranded DNA.
  Mol Biol Rep, 37, 2317-2322.  
20302647 V.Anantharaman, D.Zhang, and L.Aravind (2010).
OST-HTH: a novel predicted RNA-binding domain.
  Biol Direct, 5, 13.  
19633266 A.Gupta, P.Mehra, A.Deshmukh, A.Dar, P.Mitra, N.Roy, and S.K.Dhar (2009).
Functional dissection of the catalytic carboxyl-terminal domain of origin recognition complex subunit 1 (PfORC1) of the human malaria parasite Plasmodium falciparum.
  Eukaryot Cell, 8, 1341-1351.  
19722278 B.I.Khayrutdinov, W.J.Bae, Y.M.Yun, J.H.Lee, T.Tsuyama, J.J.Kim, E.Hwang, K.S.Ryu, H.K.Cheong, C.Cheong, J.S.Ko, T.Enomoto, P.A.Karplus, P.Güntert, S.Tada, Y.H.Jeon, and Y.Cho (2009).
Structure of the Cdt1 C-terminal domain: conservation of the winged helix fold in replication licensing factors.
  Protein Sci, 18, 2252-2264.
PDB codes: 2klo 3a4c
19344485 B.P.Duncker, I.N.Chesnokov, and B.J.McConkey (2009).
The origin recognition complex protein family.
  Genome Biol, 10, 214.  
19217277 D.B.Wigley (2009).
ORC proteins: marking the start.
  Curr Opin Struct Biol, 19, 72-78.  
19233205 G.Nimrod, A.Szilágyi, C.Leslie, and N.Ben-Tal (2009).
Identification of DNA-binding proteins using structural, electrostatic and evolutionary features.
  J Mol Biol, 387, 1040-1053.  
19416914 L.Zhang, L.Zhang, Y.Liu, S.Yang, C.Gao, H.Gong, Y.Feng, and Z.G.He (2009).
Archaeal eukaryote-like Orc1/Cdc6 initiators physically interact with DNA polymerase B1 and regulate its functions.
  Proc Natl Acad Sci U S A, 106, 7792-7797.  
19946136 M.L.Bochman, and A.Schwacha (2009).
The Mcm complex: unwinding the mechanism of a replicative helicase.
  Microbiol Mol Biol Rev, 73, 652-683.  
19762479 M.Sanchez, M.Drechsler, H.Stark, and G.Lipps (2009).
DNA translocation activity of the multifunctional replication protein ORF904 from the archaeal plasmid pRN1.
  Nucleic Acids Res, 37, 6831-6848.  
19217388 O.Danot, E.Marquenet, D.Vidal-Ingigliardi, and E.Richet (2009).
Wheel of Life, Wheel of Death: A Mechanistic Insight into Signaling by STAND Proteins.
  Structure, 17, 172-182.  
19089981 Q.Xu, C.L.Rife, D.Carlton, M.D.Miller, S.S.Krishna, M.A.Elsliger, P.Abdubek, T.Astakhova, H.J.Chiu, T.Clayton, L.Duan, J.Feuerhelm, S.K.Grzechnik, J.Hale, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, A.Kumar, D.McMullan, A.T.Morse, E.Nigoghossian, L.Okach, S.Oommachen, J.Paulsen, R.Reyes, H.van den Bedem, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2009).
Crystal structure of a novel archaeal AAA+ ATPase SSO1545 from Sulfolobus solfataricus.
  Proteins, 74, 1041-1049.
PDB code: 2fna
19000695 Q.Xu, D.McMullan, P.Abdubek, T.Astakhova, D.Carlton, C.Chen, H.J.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, M.A.Elsliger, J.Feuerhelm, J.Hale, G.W.Han, L.Jaroszewski, K.K.Jin, H.A.Johnson, H.E.Klock, M.W.Knuth, P.Kozbial, S.Sri Krishna, A.Kumar, D.Marciano, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, S.Oommachen, J.Paulsen, C.Puckett, R.Reyes, C.L.Rife, N.Sefcovic, C.Trame, H.van den Bedem, D.Weekes, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2009).
A structural basis for the regulatory inactivation of DnaA.
  J Mol Biol, 385, 368-380.
PDB code: 3bos
18650940 A.Costa, G.van Duinen, B.Medagli, J.Chong, N.Sakakibara, Z.Kelman, S.K.Nair, A.Patwardhan, and S.Onesti (2008).
Cryo-electron microscopy reveals a novel DNA-binding site on the MCM helicase.
  EMBO J, 27, 2250-2258.  
  19238189 G.T.Haugland, M.Innselset, D.Madern, and N.K.Birkeland (2008).
Characterization of the Cdc6 Homologues from the Euryarchaeon Thermoplasma acidophilum.
  Open Biochem J, 2, 129-134.  
18757887 G.T.Haugland, N.Sakakibara, A.L.Pey, C.R.Rollor, N.K.Birkeland, and Z.Kelman (2008).
Thermoplasma acidophilum Cdc6 protein stimulates MCM helicase activity by regulating its ATPase activity.
  Nucleic Acids Res, 36, 5602-5609.  
18922777 I.G.Duggin, S.A.McCallum, and S.D.Bell (2008).
Chromosome replication dynamics in the archaeon Sulfolobus acidocaldarius.
  Proc Natl Acad Sci U S A, 105, 16737-16742.  
19013274 M.L.Mott, J.P.Erzberger, M.M.Coons, and J.M.Berger (2008).
Structural synergy and molecular crosstalk between bacterial helicase loaders and replication initiators.
  Cell, 135, 623-634.
PDB codes: 3ec2 3ecc
18293358 S.Tada, L.R.Kundu, and T.Enomoto (2008).
Insight into initiator-DNA interactions: a lesson from the archaeal ORC.
  Bioessays, 30, 208-211.  
18849995 X.Zhang, and D.B.Wigley (2008).
The 'glutamate switch' provides a link between ATPase activity and ligand binding in AAA+ proteins.
  Nat Struct Mol Biol, 15, 1223-1227.  
18647841 Z.Chen, C.Speck, P.Wendel, C.Tang, B.Stillman, and H.Li (2008).
The architecture of the DNA replication origin recognition complex in Saccharomyces cerevisiae.
  Proc Natl Acad Sci U S A, 105, 10326-10331.  
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 code is shown on the right.

 

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