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protein metals links
Transferase PDB id
2au3
Jmol
Contents
Protein chain
403 a.a. *
Metals
_ZN
Waters ×169
* Residue conservation analysis
PDB id:
2au3
Name: Transferase
Title: Crystal structure of the aquifex aeolicus primase (zinc bind RNA polymerase domains)
Structure: DNA primase. Chain: a. Fragment: zinc binding and RNA polymerase domains (residues engineered: yes
Source: Aquifex aeolicus. Organism_taxid: 63363. Gene: dnag. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.205     R-free:   0.238
Authors: J.E.Corn,P.J.Pease,G.L.Hura,J.M.Berger
Key ref:
J.E.Corn et al. (2005). Crosstalk between primase subunits can act to regulate primer synthesis in trans. Mol Cell, 20, 391-401. PubMed id: 16285921 DOI: 10.1016/j.molcel.2005.09.004
Date:
26-Aug-05     Release date:   15-Nov-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O67465  (PRIM_AQUAE) -  DNA primase
Seq:
Struc: 		498 a.a.
403 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA replication   2 terms 
  Biochemical function     DNA binding     3 terms  

 

 
DOI no: 10.1016/j.molcel.2005.09.004 Mol Cell 20:391-401 (2005)
PubMed id: 16285921  
 
 
Crosstalk between primase subunits can act to regulate primer synthesis in trans.
J.E.Corn, P.J.Pease, G.L.Hura, J.M.Berger.
 
  ABSTRACT  
 
The coordination of primase function within the replisome is an essential but poorly understood feature of lagging strand synthesis. By using crystallography and small-angle X-ray scattering (SAXS), we show that functional elements of bacterial primase transition between two dominant conformations: an extended form that uncouples a regulatory domain from its associated RNA polymerase core and a compact state that sequesters the regulatory region from the site of primer synthesis. FRET studies and priming assays reveal that the regulatory domain of one primase subunit productively associates with nucleic acid that is bound to the polymerase domain of a second protomer in trans. This intersubunit interaction allows primase to select initiation sites on template DNA and implicates the regulatory domain as a "molecular brake" that restricts primer length. Our data suggest that the replisome may cooperatively use multiple primases and this conformational switch to control initiation frequency, processivity, and ultimately, Okazaki fragment synthesis.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Crystal Structure of the A. aeolicus ZBD/RPD Primase Fragment 		Figure 3.
Figure 3. FRET Studies of Labeled ZBD/RPD Constructs
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2005, 20, 391-401) copyright 2005.  
  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.  
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.  
19540940 R.D.Kuchta, and G.Stengel (2010).
Mechanism and evolution of DNA primases.
  Biochim Biophys Acta, 1804, 1180-1189.  
20350931 S.J.Lee, B.Zhu, S.M.Hamdan, and C.C.Richardson (2010).
Mechanism of sequence-specific template binding by the DNA primase of bacteriophage T7.
  Nucleic Acids Res, 38, 4372-4383.  
19703275 A.Y.Mulkidjanian, and M.Y.Galperin (2009).
On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth.
  Biol Direct, 4, 27.  
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.  
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.  
19416864 S.Geibel, S.Banchenko, M.Engel, E.Lanka, and W.Saenger (2009).
Structure and function of primase RepB' encoded by broad-host-range plasmid RSF1010 that replicates exclusively in leading-strand mode.
  Proc Natl Acad Sci U S A, 106, 7810-7815.
PDB codes: 3h20 3h25
19298182 S.M.Hamdan, and C.C.Richardson (2009).
Motors, switches, and contacts in the replisome.
  Annu Rev Biochem, 78, 205-243.  
19519900 T.Annamalai, N.Dani, B.Cheng, and Y.C.Tse-Dinh (2009).
Analysis of DNA relaxation and cleavage activities of recombinant Mycobacterium tuberculosis DNA topoisomerase I from a new expression and purification protocol.
  BMC Biochem, 10, 18.  
18653534 E.P.Sorokin, B.Cheng, S.Rathi, S.J.Aedo, M.V.Abrenica, and Y.C.Tse-Dinh (2008).
Inhibition of Mg2+ binding and DNA religation by bacterial topoisomerase I via introduction of an additional positive charge into the active site region.
  Nucleic Acids Res, 36, 4788-4796.  
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.  
18684998 M.A.Larson, R.Bressani, K.Sayood, J.E.Corn, J.M.Berger, M.A.Griep, and S.H.Hinrichs (2008).
Hyperthermophilic Aquifex aeolicus initiates primer synthesis on a limited set of trinucleotides comprised of cytosines and guanines.
  Nucleic Acids Res, 36, 5260-5269.  
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.  
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.  
18078545 C.D.Putnam, M.Hammel, G.L.Hura, and J.A.Tainer (2007).
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.
  Q Rev Biophys, 40, 191-285.  
17637338 J.E.Corn, and J.M.Berger (2007).
FASTDXL: a generalized screen to trap disulfide-stabilized complexes for use in structural studies.
  Structure, 15, 773-780.  
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.  
17286576 N.Ito, I.Matsui, and E.Matsui (2007).
Molecular basis for the subunit assembly of the primase from an archaeon Pyrococcus horikoshii.
  FEBS J, 274, 1340-1351.
PDB code: 2dla
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
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.  
16720577 K.Fien, and J.Hurwitz (2006).
Fission yeast Mcm10p contains primase activity.
  J Biol Chem, 281, 22248-22260.  
16935884 T.Lionnet, A.Dawid, S.Bigot, F.X.Barre, O.A.Saleh, F.Heslot, J.F.Allemand, D.Bensimon, and V.Croquette (2006).
DNA mechanics as a tool to probe helicase and translocase activity.
  Nucleic Acids Res, 34, 4232-4244.  
16642036 U.Qimron, S.J.Lee, S.M.Hamdan, and C.C.Richardson (2006).
Primer initiation and extension by T7 DNA primase.
  EMBO J, 25, 2199-2208.  
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
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.