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PDBsum entry 1d0q
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protein metals Protein-protein interface(s) links
Transferase PDB id
1d0q

 

 

 

 

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Contents
Protein chains
102 a.a. *
Metals
_ZN ×2
Waters ×162
* Residue conservation analysis
PDB id:
1d0q
Name: Transferase
Title: Structure of the zinc-binding domain of bacillus stearothermophilus DNA primase
Structure: DNA primase. Chain: a, b. Fragment: zinc-binding domain. Engineered: yes
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: geobacillus stearothermophilus. Expression_system_taxid: 1422.
Biol. unit: Dimer (from PQS)
Resolution:
1.71Å     R-factor:   0.204     R-free:   0.225
Authors: H.Pan,D.B.Wigley
Key ref:
H.Pan and D.B.Wigley (2000). Structure of the zinc-binding domain of Bacillus stearothermophilus DNA primase. Structure, 8, 231-239. PubMed id: 10745010 DOI: 10.1016/S0969-2126(00)00101-5
Date:
14-Sep-99     Release date:   29-Mar-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9X4D0  (DNAG_GEOSE) -  DNA primase from Geobacillus stearothermophilus
Seq:
Struc: 		 
Seq:
Struc: 		597 a.a.
102 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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/S0969-2126(00)00101-5 Structure 8:231-239 (2000)
PubMed id: 10745010  
 
 
Structure of the zinc-binding domain of Bacillus stearothermophilus DNA primase.
H.Pan, D.B.Wigley.
 
  ABSTRACT  
 
BACKGROUND: DNA primases catalyse the synthesis of the short RNA primers that are required for DNA replication by DNA polymerases. Primases comprise three functional domains: a zinc-binding domain that is responsible for template recognition, a polymerase domain, and a domain that interacts with the replicative helicase, DnaB. RESULTS: We present the crystal structure of the zinc-binding domain of DNA primase from Bacillus stearothermophilus, determined at 1.7 A resolution. This is the first high-resolution structural information about any DNA primase. A model is discussed for the interaction of this domain with the single-stranded DNA template. CONCLUSIONS: The structure of the DNA primase zinc-binding domain confirms that the protein belongs to the zinc ribbon subfamily. Structural comparison with other nucleic acid binding proteins suggests that the beta sheet of primase is likely to be the DNA-binding surface, with conserved residues on this surface being involved in the binding and recognition of DNA.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Structural comparison of members of the zinc ribbon family. (a) TFIIB, (b) TFIIS, (c) RPB9 and (d) DNA primase P12. The zinc ions are shown as a white ball.
 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 231-239) copyright 2000.  
  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.  
20511586 K.Beck, A.Vannini, P.Cramer, and G.Lipps (2010).
The archaeo-eukaryotic primase of plasmid pRN1 requires a helix bundle domain for faithful primer synthesis.
  Nucleic Acids Res, 38, 6707-6718.
PDB code: 3m1m
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.  
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.  
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.  
16788176 S.A.Koepsell, M.A.Larson, M.A.Griep, and S.H.Hinrichs (2006).
Staphylococcus aureus helicase but not Escherichia coli helicase stimulates S. aureus primase activity and maintains initiation specificity.
  J Bacteriol, 188, 4673-4680.  
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
15649896 A.J.Oakley, K.V.Loscha, P.M.Schaeffer, E.Liepinsh, G.Pintacuda, M.C.Wilce, G.Otting, and N.E.Dixon (2005).
Crystal and solution structures of the helicase-binding domain of Escherichia coli primase.
  J Biol Chem, 280, 11495-11504.
PDB code: 1t3w
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
15837199 K.Syson, J.Thirlway, A.M.Hounslow, P.Soultanas, and J.P.Waltho (2005).
Solution structure of the helicase-interaction domain of the primase DnaG: a model for helicase activation.
  Structure, 13, 609-616.
PDB code: 1z8s
16027112 L.M.Iyer, E.V.Koonin, D.D.Leipe, and L.Aravind (2005).
Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members.
  Nucleic Acids Res, 33, 3875-3896.  
15939015 P.Soultanas (2005).
The bacterial helicase-primase interaction: a common structural/functional module.
  Structure, 13, 839-844.  
16273105 S.H.Lao-Sirieix, R.K.Nookala, P.Roversi, S.D.Bell, and L.Pellegrini (2005).
Structure of the heterodimeric core primase.
  Nat Struct Mol Biol, 12, 1137-1144.
PDB code: 1zt2
15173380 J.Thirlway, I.J.Turner, C.T.Gibson, L.Gardiner, K.Brady, S.Allen, C.J.Roberts, and P.Soultanas (2004).
DnaG interacts with a linker region that joins the N- and C-domains of DnaB and induces the formation of 3-fold symmetric rings.
  Nucleic Acids Res, 32, 2977-2986.  
12769857 M.Kato, T.Ito, G.Wagner, C.C.Richardson, and T.Ellenberger (2003).
Modular architecture of the bacteriophage T7 primase couples RNA primer synthesis to DNA synthesis.
  Mol Cell, 11, 1349-1360.
PDB code: 1nui
11395402 D.N.Frick, and C.C.Richardson (2001).
DNA primases.
  Annu Rev Biochem, 70, 39-80.  
11572774 J.S.Stamler, S.Lamas, and F.C.Fang (2001).
Nitrosylation. the prototypic redox-based signaling mechanism.
  Cell, 106, 675-683.  
10712935 J.L.Keck, and J.M.Berger (2000).
DNA replication at high resolution.
  Chem Biol, 7, R63-R71.  
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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