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PDBsum entry 1z8s
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Transferase PDB id
1z8s

 

 

 

 

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Contents
Protein chain
146 a.a. *
* Residue conservation analysis
PDB id:
1z8s
Name: Transferase
Title: Dnab binding domain of dnag (p16) from bacillus stearothermophilus (residues 452-597)
Structure: DNA primase. Chain: a. Fragment: p16, residues 451-597. Engineered: yes
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: dnag. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 10 models
Authors: K.Syson,J.Thirlway,A.M.Hounslow,P.Soultanas,J.P.Waltho
Key ref:
K.Syson et al. (2005). Solution structure of the helicase-interaction domain of the primase DnaG: a model for helicase activation. Structure, 13, 609-616. PubMed id: 15837199 DOI: 10.1016/j.str.2005.01.022
Date:
31-Mar-05     Release date:   04-Oct-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9X4D0  (DNAG_GEOSE) -  DNA primase from Geobacillus stearothermophilus
Seq:
Struc: 		 
Seq:
Struc: 		597 a.a.
146 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.101  - Dna primase DnaG.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ssDNA + n NTP = ssDNA/pppN(pN)n-1 hybrid + (n-1) diphosphate
ssDNA
 + n NTP
 = ssDNA/pppN(pN)n-1 hybrid
 + (n-1) diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Key reference    
 
 
DOI no: 10.1016/j.str.2005.01.022 Structure 13:609-616 (2005)
PubMed id: 15837199  
 
 
Solution structure of the helicase-interaction domain of the primase DnaG: a model for helicase activation.
K.Syson, J.Thirlway, A.M.Hounslow, P.Soultanas, J.P.Waltho.
 
  ABSTRACT  
 
The helicase-primase interaction is a critical event in DNA replication and is mediated by a putative helicase-interaction domain within the primase. The solution structure of the helicase-interaction domain of DnaG reveals that it is made up of two independent subdomains: an N-terminal six-helix module and a C-terminal two-helix module that contains the residues of the primase previously identified as important in the interaction with the helicase. We show that the two-helix module alone is sufficient for strong binding between the primase and the helicase but fails to activate the helicase; both subdomains are required for helicase activation. The six-helix module of the primase has only one close structural homolog, the N-terminal domain of the corresponding helicase. This surprising structural relationship, coupled with the differences in surface properties of the two molecules, suggests how the helicase-interaction domain may perturb the structure of the helicase and lead to activation.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. A Model for the DnaB-P16 Interaction
(A) The 3-fold symmetric ring of hexameric DnaB, showing the N-domain of one monomer (6N) interacting with the C-domain (5H) of the neighboring monomer (Yang et al., 2003).
(B) In the DnaB-P16 complex, the P16 protein (shaded purple) interacts with the linker region that connects the N-terminal (6N) and C-terminal (6H) domains of one monomer, via its C2 subdomain. In addition, the C1 subdomain displaces 6N while at the same time maintaining the interactions with 5H that are essential to preserve a 3-fold symmetric ring in the helicase-primase complex.
 
  The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 609-616) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20348261 J.Li, J.Liu, L.Zhou, H.Pei, J.Zhou, and H.Xiang (2010).
Two distantly homologous DnaG primases from Thermoanaerobacter tengcongensis exhibit distinct initiation specificities and priming activities.
  J Bacteriol, 192, 2670-2681.  
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.  
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
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.  
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
17367384 K.Chintakayala, M.A.Larson, W.H.Grainger, D.J.Scott, M.A.Griep, S.H.Hinrichs, and P.Soultanas (2007).
Domain swapping reveals that the C- and N-terminal domains of DnaG and DnaB, respectively, are functional homologues.
  Mol Microbiol, 63, 1629-1639.  
17947583 S.Bailey, W.K.Eliason, and T.A.Steitz (2007).
Structure of hexameric DnaB helicase and its complex with a domain of DnaG primase.
  Science, 318, 459-463.
PDB codes: 2r6a 2r6c 2r6d 2r6e
17606462 S.Bailey, W.K.Eliason, and T.A.Steitz (2007).
The crystal structure of the Thermus aquaticus DnaB helicase monomer.
  Nucleic Acids Res, 35, 4728-4736.
PDB code: 2q6t
16935873 J.E.Corn, and J.M.Berger (2006).
Regulation of bacterial priming and daughter strand synthesis through helicase-primase interactions.
  Nucleic Acids Res, 34, 4082-4088.  
16452437 J.Thirlway, and P.Soultanas (2006).
In the Bacillus stearothermophilus DnaB-DnaG complex, the activities of the two proteins are modulated by distinct but overlapping networks of residues.
  J Bacteriol, 188, 1534-1539.  
17010164 X.C.Su, P.M.Schaeffer, K.V.Loscha, P.H.Gan, N.E.Dixon, and G.Otting (2006).
Monomeric solution structure of the helicase-binding domain of Escherichia coli DnaG primase.
  FEBS J, 273, 4997-5009.
PDB code: 2haj
16285921 J.E.Corn, P.J.Pease, G.L.Hura, and J.M.Berger (2005).
Crosstalk between primase subunits can act to regulate primer synthesis in trans.
  Mol Cell, 20, 391-401.
PDB code: 2au3
15939015 P.Soultanas (2005).
The bacterial helicase-primase interaction: a common structural/functional module.
  Structure, 13, 839-844.  
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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