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PDBsum entry 1zt2
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protein ligands metals Protein-protein interface(s) links
Replication, transferase PDB id
1zt2

 

 

 

 

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Contents
Protein chains
327 a.a. *
207 a.a. *
Ligands
SO4 ×39
Metals
_ZN ×2
Waters ×12
* Residue conservation analysis
PDB id:
1zt2
Name: Replication, transferase
Title: Heterodimeric structure of the core primase.
Structure: DNA primase small subunit. Chain: a, c. Engineered: yes. DNA primase large subunit. Chain: b, d. Fragment: residues 1-212. Engineered: yes
Source: Sulfolobus solfataricus. Organism_taxid: 2287. Gene: pria. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: prib.
Biol. unit: Dimer (from PQS)
Resolution:
3.33Å     R-factor:   0.236     R-free:   0.243
Authors: S.H.Lao-Sirieix,R.K.Nookala,P.Roversi,S.D.Bell,L.Pellegrini
Key ref:
S.H.Lao-Sirieix et al. (2005). Structure of the heterodimeric core primase. Nat Struct Mol Biol, 12, 1137-1144. PubMed id: 16273105 DOI: 10.1038/nsmb1013
Date:
26-May-05     Release date:   08-Nov-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Q97Z83  (PRIS_SULSO) -  DNA primase small subunit PriS from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Seq:
Struc: 		330 a.a.
327 a.a.
Protein chains
Q9UWW1  (PRIL_SULSO) -  DNA primase large subunit PriL from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Seq:
Struc: 		307 a.a.
207 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, C, B, D: E.C.2.7.7.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1038/nsmb1013 Nat Struct Mol Biol 12:1137-1144 (2005)
PubMed id: 16273105  
 
 
Structure of the heterodimeric core primase.
S.H.Lao-Sirieix, R.K.Nookala, P.Roversi, S.D.Bell, L.Pellegrini.
 
  ABSTRACT  
 
Primases are DNA-dependent RNA polymerases that synthesize the oligoribonucleotide primers essential to DNA replication. In archaeal and eukaryotic organisms, the core primase is a heterodimeric enzyme composed of a small and a large subunit. Here we report a crystallographic and biochemical analysis of the core primase from the archaeon Sulfolobus solfataricus. The structure provides the first three-dimensional description of the large subunit and its interaction with the small subunit. The evolutionary conservation of amino acids at the protein-protein interface implies that the observed mode of subunit association is conserved among archaeal and eukaryotic primases. The orientation of the large subunit in the core primase probably excludes its direct involvement in catalysis. Modeling of a DNA-RNA helix together with structure-based site-directed mutagenesis provides insight into the mechanism of template DNA binding and RNA primer synthesis.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Analysis of the PriS-PriL interface. (a) Hydrophilic interactions at the PriS-PriL interface. Hydrogen bonds are yellow dashed lines. The carbonyl groups of Asp162 and Asp163 at the C terminus of PriS helix 4 are hydrogen-bonded to the main chain amides of PriL residues Lys165 and Gly166. The side chains of Asp162 and Asp163 further interact electrostatically with Arg224 and Arg227. (b) Structure-based yeast two-hybrid analysis of the Sso PriS-PriL interface. Single and double mutations in PriS and PriL disrupt the interaction between the core primase subunits. Control plate: -Leu, -Trp; selective plates: -Leu, -Trp, -His and the more stringent -Leu, -Trp, -His, -Adenine. Numbered samples are identified in Table 1. 		Figure 6.
Figure 6. Interaction of the Sso core primase with DNA template and RNA primer. (a) The zinc-binding motif of archaeal primases. The small subunits of Sso, Pho (PDB entry 1V33) and Sis (PDB entry 1RNI) primases were superimposed. The Sso PriS-prim is shown as a molecular surface. The zinc-binding motifs of Sso (green), Pho (yellow) and Sis (pink) are narrow tubes and their zinc atoms are spheres. (b) Comparison of the enzymatic activity of wild-type Sso core primase (Pri-WT) with that of the RR and SNG mutants (Pri-RR and Pri-SNG, respectively). Experiments were performed as for Figure 1c. DN, dinucleotide product. (c) Comparison of the quantities of product synthesized by Pri-WT and the RR and SNG mutants. Experiments were performed as for Figure 1c, with 1.2 M primase concentration. The radiolabeled products were quantified by filter binding and liquid scintillation counting. Each bar represents the average of five independent values with s.e.m. indicated. (d) Model of the Sso core primase-DNA template-RNA primer complex. The protein component of the complex is depicted as a molecular surface. The phosphate backbones of DNA and RNA are orange and cyan tubes, respectively. The proposed trajectory of the template DNA across the surface of the core primase is drawn. The position of PriS-Zn and the putative position of PriL-CTD are indicated by solid and dashed circles, respectively. The side chains of basic residues on and near PriL 5 are blue. The positions of PriL residues Arg84 and Arg85 are indicated.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2005, 12, 1137-1144) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21265766 S.A.MacNeill (2011).
Protein-protein interactions in the archaeal core replisome.
  Biochem Soc Trans, 39, 163-168.  
20385010 A.Swiatek, and S.A.Macneill (2010).
The archaeo-eukaryotic GINS proteins and the archaeal primase catalytic subunit PriS share a common domain.
  Biol Direct, 5, 17.  
20163964 E.Johansson, and S.A.Macneill (2010).
The eukaryotic replicative DNA polymerases take shape.
  Trends Biochem Sci, 35, 339-347.  
  20944230 H.L.Axelrod, D.Das, P.Abdubek, T.Astakhova, C.Bakolitsa, D.Carlton, C.Chen, H.J.Chiu, T.Clayton, M.C.Deller, L.Duan, K.Ellrott, C.L.Farr, J.Feuerhelm, J.C.Grant, A.Grzechnik, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, A.Kumar, W.W.Lam, D.Marciano, D.McMullan, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, C.Puckett, R.Reyes, N.Sefcovic, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, T.Wooten, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1335-1346.
PDB codes: 2glz 2gvi 3d00
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
20404922 L.Sauguet, S.Klinge, R.L.Perera, J.D.Maman, and L.Pellegrini (2010).
Shared active site architecture between the large subunit of eukaryotic primase and DNA photolyase.
  PLoS One, 5, e10083.
PDB code: 3lgb
19540940 R.D.Kuchta, and G.Stengel (2010).
Mechanism and evolution of DNA primases.
  Biochim Biophys Acta, 1804, 1180-1189.  
20643958 S.Vaithiyalingam, E.M.Warren, B.F.Eichman, and W.J.Chazin (2010).
Insights into eukaryotic DNA priming from the structure and functional interactions of the 4Fe-4S cluster domain of human DNA primase.
  Proc Natl Acad Sci U S A, 107, 13684-13689.
PDB code: 3l9q
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
17893144 B.E.Weiner, H.Huang, B.M.Dattilo, M.J.Nilges, E.Fanning, and W.J.Chazin (2007).
An iron-sulfur cluster in the C-terminal domain of the p58 subunit of human DNA primase.
  J Biol Chem, 282, 33444-33451.  
17709343 K.Beck, and G.Lipps (2007).
Properties of an unusual DNA primase from an archaeal plasmid.
  Nucleic Acids Res, 35, 5635-5645.  
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
17704817 S.Klinge, J.Hirst, J.D.Maman, T.Krude, and L.Pellegrini (2007).
An iron-sulfur domain of the eukaryotic primase is essential for RNA primer synthesis.
  Nat Struct Mol Biol, 14, 875-877.  
17158702 E.R.Barry, and S.D.Bell (2006).
DNA replication in the archaea.
  Microbiol Mol Biol Rev, 70, 876-887.  
16467299 I.G.Duggin, and S.D.Bell (2006).
The chromosome replication machinery of the archaeon Sulfolobus solfataricus.
  J Biol Chem, 281, 15029-15032.  
16816388 L.Yakovleva, and S.Shuman (2006).
Nucleotide misincorporation, 3'-mismatch extension, and responses to abasic sites and DNA adducts by the polymerase component of bacterial DNA ligase D.
  J Biol Chem, 281, 25026-25040.  
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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