PDBsum entry 2r6d

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protein Protein-protein interface(s) links
Replication PDB id
Protein chains
405 a.a. *
376 a.a. *
* Residue conservation analysis
PDB id:
Name: Replication
Title: Crystal form b1
Structure: Replicative helicase. Chain: a, b, c, d, e, f. Synonym: dnab helicase. Engineered: yes
Source: Bacillus stearothermophilus. Gene: dnab. Expressed in: escherichia coli.
3.70Å     R-factor:   0.310     R-free:   0.322
Authors: S.Bailey,W.K.Eliason,T.A.Steitz
Key ref:
S.Bailey et al. (2007). Structure of hexameric DnaB helicase and its complex with a domain of DnaG primase. Science, 318, 459-463. PubMed id: 17947583 DOI: 10.1126/science.1147353
05-Sep-07     Release date:   10-Jun-08    
Go to PROCHECK summary

Protein chains
No UniProt id for this chain
Struc: 405 a.a.
Protein chains
No UniProt id for this chain
Struc: 376 a.a.
Key:    Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA replication   2 terms 
  Biochemical function     protein binding     6 terms  


DOI no: 10.1126/science.1147353 Science 318:459-463 (2007)
PubMed id: 17947583  
Structure of hexameric DnaB helicase and its complex with a domain of DnaG primase.
S.Bailey, W.K.Eliason, T.A.Steitz.
The complex between the DnaB helicase and the DnaG primase unwinds duplex DNA at the eubacterial replication fork and synthesizes the Okazaki RNA primers. The crystal structures of hexameric DnaB and its complex with the helicase binding domain (HBD) of DnaG reveal that within the hexamer the two domains of DnaB pack with strikingly different symmetries to form a distinct two-layered ring structure. Each of three bound HBDs stabilizes the DnaB hexamer in a conformation that may increase its processivity. Three positive, conserved electrostatic patches on the N-terminal domain of DnaB may also serve as a binding site for DNA and thereby guide the DNA to a DnaG active site.
  Selected figure(s)  
Figure 1.
Fig. 1. Architecture of the DnaB hexamer. (A) Experimentally phased and cross-crystal averaged electron density maps of the four DnaB crystal forms. Shown at the foot of each map is the high-resolution limit at which each map was calculated. (B) "Side" view, orthogonal to the ring axis, of a ribbon representation of the DnaB hexamer. The NTD, CTD, and linker region are colored blue, red, and yellow respectively. (C) "Top" view, looking down the ring axis, of the DnaB hexamer. The CTDs are shown in a surface representation; the NTDs are shown as ribbons. Those subunits whose NTDs lie on the inner surface of the ring are colored as in (B), and those on the outer surface of the ring are colored white. (D) "Side" view of the two distinct conformations of the DnaB subunits within the hexamer, colored as in (B). Adjacent CTDs interacting with the linker region are shown as white surface representations.
Figure 3.
Fig. 3. Structure of the complex between DnaB and HBD. (A) (Top) "Top" view of a ribbon representation of the complex showing the three HBDs (green) bound at the periphery of the NTD collar (light blue and blue). The CTD and linker region are colored red and yellow, respectively. (Bottom) The interface between DnaB and HBD shown as ribbons with a transparent surface. (B) "Side" view of a surface representation of the complex revealing no interaction between the HBDs (green) and the DnaB CTD (red) or linker region (yellow). (C) Backbone trace of the HBD DnaB interface, residues known to modulate the interaction between DnaB and DnaG, are shown as colored spheres.
  The above figures are reprinted by permission from the AAAs: Science (2007, 318, 459-463) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20462378 A.M.van Oijen, and J.J.Loparo (2010).
Single-molecule studies of the replisome.
  Annu Rev Biophys, 39, 429-448.  
19917723 C.Lee, I.Liachko, R.Bouten, Z.Kelman, and B.K.Tye (2010).
Alternative mechanisms for coordinating polymerase alpha and MCM helicase.
  Mol Cell Biol, 30, 423-435.  
20525790 G.S.Briggs, J.Yu, A.A.Mahdi, and R.G.Lloyd (2010).
The RdgC protein employs a novel mechanism involving a finger domain to bind to circular DNA.
  Nucleic Acids Res, 38, 6433-6446.  
20591822 M.A.Larson, M.A.Griep, R.Bressani, K.Chintakayala, P.Soultanas, and S.H.Hinrichs (2010).
Class-specific restrictions define primase interactions with DNA template and replicative helicase.
  Nucleic Acids Res, 38, 7167-7178.  
20129058 M.Makowska-Grzyska, and J.M.Kaguni (2010).
Primase directs the release of DnaC from DnaB.
  Mol Cell, 37, 90.  
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.  
  21129204 T.C.Mueser, J.M.Hinerman, J.M.Devos, R.A.Boyer, and K.J.Williams (2010).
Structural analysis of bacteriophage T4 DNA replication: a review in the Virology Journal series on bacteriophage T4 and its relatives.
  Virol J, 7, 359.  
20192763 W.Yang (2010).
Lessons learned from UvrD helicase: mechanism for directional movement.
  Annu Rev Biophys, 39, 367-385.  
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
19574219 B.Zhu, S.J.Lee, and C.C.Richardson (2009).
An in trans interaction at the interface of the helicase and primase domains of the hexameric gene 4 protein of bacteriophage T7 modulates their activities.
  J Biol Chem, 284, 23842-23851.  
19477652 D.Aiello, M.H.Barnes, E.E.Biswas, S.B.Biswas, S.Gu, J.D.Williams, T.L.Bowlin, and D.T.Moir (2009).
Discovery, characterization and comparison of inhibitors of Bacillus anthracis and Staphylococcus aureus replicative DNA helicases.
  Bioorg Med Chem, 17, 4466-4476.  
19415803 K.Chintakayala, C.Machón, A.Haroniti, M.A.Larson, S.H.Hinrichs, M.A.Griep, and P.Soultanas (2009).
Allosteric regulation of the primase (DnaG) activity by the clamp-loader (tau) in vitro.
  Mol Microbiol, 72, 537-549.  
19255093 K.V.Loscha, K.Jaudzems, C.Ioannou, X.C.Su, F.R.Hill, G.Otting, N.E.Dixon, and E.Liepinsh (2009).
A novel zinc-binding fold in the helicase interaction domain of the Bacillus subtilis DnaI helicase loader.
  Nucleic Acids Res, 37, 2395-2404.
PDB code: 2k7r
19474351 M.Samuels, G.Gulati, J.H.Shin, R.Opara, E.McSweeney, M.Sekedat, S.Long, Z.Kelman, and D.Jeruzalmi (2009).
A biochemically active MCM-like helicase in Bacillus cereus.
  Nucleic Acids Res, 37, 4441-4452.  
19583259 S.B.Biswas, E.Wydra, and E.E.Biswas (2009).
Mechanisms of DNA binding and regulation of Bacillus anthracis DNA primase.
  Biochemistry, 48, 7373-7382.  
19298182 S.M.Hamdan, and C.C.Richardson (2009).
Motors, switches, and contacts in the replisome.
  Annu Rev Biochem, 78, 205-243.  
19841750 T.Kashav, R.Nitharwal, S.A.Abdulrehman, A.Gabdoulkhakov, W.Saenger, S.K.Dhar, and S.Gourinath (2009).
Three-dimensional structure of N-terminal domain of DnaB helicase and helicase-primase interactions in Helicobacter pylori.
  PLoS One, 4, e7515.
PDB code: 3gxv
19074952 Y.H.Lo, K.L.Tsai, Y.J.Sun, W.T.Chen, C.Y.Huang, and C.D.Hsiao (2009).
The crystal structure of a replicative hexameric helicase DnaC and its complex with single-stranded DNA.
  Nucleic Acids Res, 37, 804-814.
PDB codes: 2vye 2vyf
18801730 D.M.Kanter, I.Bruck, and D.L.Kaplan (2008).
Mcm subunits can assemble into two different active unwinding complexes.
  J Biol Chem, 283, 31172-31182.  
18329872 E.J.Enemark, and L.Joshua-Tor (2008).
On helicases and other motor proteins.
  Curr Opin Struct Biol, 18, 243-257.  
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.  
18157148 G.Wang, M.G.Klein, E.Tokonzaba, Y.Zhang, L.G.Holden, and X.S.Chen (2008).
The structure of a DnaB-family replicative helicase and its interactions with primase.
  Nat Struct Mol Biol, 15, 94.
PDB codes: 3bgw 3bh0
18193061 J.E.Corn, J.G.Pelton, and J.M.Berger (2008).
Identification of a DNA primase template tracking site redefines the geometry of primer synthesis.
  Nat Struct Mol Biol, 15, 163-169.
PDB code: 3b39
18366438 K.Chintakayala, M.A.Larson, M.A.Griep, S.H.Hinrichs, and P.Soultanas (2008).
Conserved residues of the C-terminal p16 domain of primase are involved in modulating the activity of the bacterial primosome.
  Mol Microbiol, 68, 360-371.  
18250630 K.J.Marians (2008).
Understanding how the replisome works.
  Nat Struct Mol Biol, 15, 125-127.  
19019158 L.E.Bingle, K.V.Rajasekar, S.Muntaha, V.Nadella, E.I.Hyde, and C.M.Thomas (2008).
A single aromatic residue in transcriptional repressor protein KorA is critical for cooperativity with its co-regulator KorB.
  Mol Microbiol, 70, 1502-1514.  
18223657 N.A.Tanner, S.M.Hamdan, S.Jergic, P.M.Schaeffer, N.E.Dixon, and A.M.van Oijen (2008).
Single-molecule studies of fork dynamics in Escherichia coli DNA replication.
  Nat Struct Mol Biol, 15, 170-176.  
18647240 N.D.Thomsen, and J.M.Berger (2008).
Structural frameworks for considering microbial protein- and nucleic acid-dependent motor ATPases.
  Mol Microbiol, 69, 1071-1090.  
18937104 R.D.Shereda, A.G.Kozlov, T.M.Lohman, M.M.Cox, and J.L.Keck (2008).
SSB as an organizer/mobilizer of genome maintenance complexes.
  Crit Rev Biochem Mol Biol, 43, 289-318.  
18452509 S.A.Koepsell, M.A.Larson, C.A.Frey, S.H.Hinrichs, and M.A.Griep (2008).
Staphylococcus aureus primase has higher initiation specificity, interacts with single-stranded DNA stronger, but is less stimulated by its helicase than Escherichia coli primase.
  Mol Microbiol, 68, 1570-1582.  
18479467 T.Biswas, and O.V.Tsodikov (2008).
Hexameric ring structure of the N-terminal domain of Mycobacterium tuberculosis DnaB helicase.
  FEBS J, 275, 3064-3071.
PDB code: 2r5u
18593709 Y.Matsushima, C.L.Farr, L.Fan, and L.S.Kaguni (2008).
Physiological and biochemical defects in carboxyl-terminal mutants of mitochondrial DNA helicase.
  J Biol Chem, 283, 23964-23971.  
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.