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PDBsum entry 2ex3
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protein metals Protein-protein interface(s) links
Transferase/replication PDB id
2ex3

 

 

 

 

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Contents
Protein chains
(+ 0 more) 570 a.a. *
(+ 0 more) 196 a.a. *
Metals
_PB ×16
* Residue conservation analysis
PDB id:
2ex3
Name: Transferase/replication
Title: Bacteriophage phi29 DNA polymerase bound to terminal protein
Structure: DNA polymerase. Chain: a, c, e, g, i, k. Synonym: early protein gp2. Engineered: yes. Mutation: yes. DNA terminal protein. Chain: b, d, f, h, j, l. Fragment: terminal protein. Synonym: protein gp3.
Source: Bacillus phage phi29. Organism_taxid: 10756. Gene: 2. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: 3. Expressed in: bacillus subtilis. Expression_system_taxid: 1423
Biol. unit: Dimer (from PQS)
Resolution:
3.00Å     R-factor:   0.203     R-free:   0.229
Authors: S.Kamtekar,A.J.Berman,J.Wang,M.De Vega,L.Blanco,M.Salas,T.A.Steitz
Key ref:
S.Kamtekar et al. (2006). The phi29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition. EMBO J, 25, 1335-1343. PubMed id: 16511564 DOI: 10.1038/sj.emboj.7601027
Date:
07-Nov-05     Release date:   14-Mar-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P03680  (DPOL_BPPH2) -  DNA polymerase from Bacillus phage phi29
Seq:
Struc: 		 
Seq:
Struc: 		575 a.a.
570 a.a.*
Protein chains
Pfam   ArchSchema ?
P03681  (TERM_BPPH2) -  Primer terminal protein from Bacillus phage phi29
Seq:
Struc: 		266 a.a.
196 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 36 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: Chains A, C, E, G, I, K: E.C.2.7.7.7  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
DNA(n)
 + 2'-deoxyribonucleoside 5'-triphosphate
 = DNA(n+1)
 + diphosphate
   Enzyme class 3: Chains A, C, E, G, I, K: E.C.3.1.11.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
   Enzyme class 4: Chains B, D, F, H, J, L: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1038/sj.emboj.7601027 EMBO J 25:1335-1343 (2006)
PubMed id: 16511564  
 
 
The phi29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition.
S.Kamtekar, A.J.Berman, J.Wang, J.M.Lázaro, M.de Vega, L.Blanco, M.Salas, T.A.Steitz.
 
  ABSTRACT  
 
The absolute requirement for primers in the initiation of DNA synthesis poses a problem for replicating the ends of linear chromosomes. The DNA polymerase of bacteriophage phi29 solves this problem by using a serine hydroxyl of terminal protein to prime replication. The 3.0 A resolution structure shows one domain of terminal protein making no interactions, a second binding the polymerase and a third domain containing the priming serine occupying the same binding cleft in the polymerase as duplex DNA does during elongation. Thus, the progressively elongating DNA duplex product must displace this priming domain. Further, this heterodimer of polymerase and terminal protein cannot accommodate upstream template DNA, thereby explaining its specificity for initiating DNA synthesis only at the ends of the bacteriophage genome. We propose a model for the transition from the initiation to the elongation phases in which the priming domain of terminal protein moves out of the active site as polymerase elongates the primer strand. The model indicates that terminal protein should dissociate from polymerase after the incorporation of approximately six nucleotides.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Electron density for a helix of terminal protein near the active site of polymerase. On the left is a 3.5 Å resolution map contoured at 1 using data from the I23 crystal form. It was calculated using amplitudes sharpened by a factor of 100 and experimentally phased with solvent-flattened heavy-atom phases. Side chains cannot be unambiguously assigned in this map. On the right is a composite omit map contoured at 1 and calculated to 3 Å using data from the C2 crystal form. Side chain density is much better defined in this map. Figures 1, 2, 3A, 3B, and 4 were made using Pymol (http://www.pymol.org). 		Figure 2.
Figure 2 The structure of the polymerase:terminal protein heterodimer. (A) A ribbon representation, with polymerase colored according to Kamtekar et al, 2004, and terminal protein shown with cylindrical helices. (B) A view of the complex rotated 90° from that shown in (A), with terminal protein shown as cylinders underneath a transparent surface. (C) A C[ ]trace of polymerase from the polymerase:terminal protein complex (in color) superimposed on the apo polymerase structure. Significant differences in conformation occur only in a loop between residues 304 and 314 (shown in magenta in the complex and in black in the apo polymerase structure). The polymerase active site is marked by the space-filling representations of the carboxylates that coordinate the catalytic metal ions. (D) Terminal protein in the same orientation as in (B).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 1335-1343) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20505767 A.Arias, C.Perales, C.Escarmís, and E.Domingo (2010).
Deletion mutants of VPg reveal new cytopathology determinants in a picornavirus.
  PLoS One, 5, e10735.  
20823229 D.Muñoz-Espín, I.Holguera, D.Ballesteros-Plaza, R.Carballido-López, and M.Salas (2010).
Viral terminal protein directs early organization of phage DNA replication at the bacterial nucleoid.
  Proc Natl Acad Sci U S A, 107, 16548-16553.  
20675469 S.Kolkenbrock, B.Naumann, M.Hippler, and S.Fetzner (2010).
A novel replicative enzyme encoded by the linear Arthrobacter plasmid pAL1.
  J Bacteriol, 192, 4935-4943.  
19033368 I.Rodríguez, J.M.Lázaro, M.Salas, and M.de Vega (2009).
Involvement of the TPR2 subdomain movement in the activities of phi29 DNA polymerase.
  Nucleic Acids Res, 37, 193-203.  
19801157 J.Pan, L.Lin, and Y.J.Tao (2009).
Self-guanylylation of birnavirus VP1 does not require an intact polymerase activity site.
  Virology, 395, 87-96.  
19486296 T.Tenson, and V.Hauryliuk (2009).
Does the ribosome have initiation and elongation modes of translation?
  Mol Microbiol, 72, 1310-1315.  
19011105 E.Longás, L.Villar, J.M.Lázaro, M.de Vega, and M.Salas (2008).
Phage phi29 and Nf terminal protein-priming domain specifies the internal template nucleotide to initiate DNA replication.
  Proc Natl Acad Sci U S A, 105, 18290-18295.  
18674782 J.S.Koti, M.C.Morais, R.Rajagopal, B.A.Owen, C.T.McMurray, and D.L.Anderson (2008).
DNA packaging motor assembly intermediate of bacteriophage phi29.
  J Mol Biol, 381, 1114-1132.  
18948533 K.J.Durniak, S.Bailey, and T.A.Steitz (2008).
The structure of a transcribing T7 RNA polymerase in transition from initiation to elongation.
  Science, 322, 553-557.
PDB codes: 3e2e 3e3j
19006816 K.Porter, and M.L.Dyall-Smith (2008).
Transfection of haloarchaea by the DNAs of spindle and round haloviruses and the use of transposon mutagenesis to identify non-essential regions.
  Mol Microbiol, 70, 1236-1245.  
18606992 Y.Xiang, M.C.Morais, D.N.Cohen, V.D.Bowman, D.L.Anderson, and M.G.Rossmann (2008).
Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage phi29 tail.
  Proc Natl Acad Sci U S A, 105, 9552-9557.
PDB codes: 3csq 3csr 3csz 3ct0 3ct1 3ct5
17611604 A.J.Berman, S.Kamtekar, J.L.Goodman, J.M.Lázaro, M.de Vega, L.Blanco, M.Salas, and T.A.Steitz (2007).
Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases.
  EMBO J, 26, 3494-3505.
PDB codes: 2py5 2pyj 2pyl 2pzs
17326804 A.Stoll, M.Redenbach, and J.Cullum (2007).
Identification of essential genes for linear replication of an SCP1 composite plasmid.
  FEMS Microbiol Lett, 270, 146-154.  
18496613 M.Garcia-Diaz, and K.Bebenek (2007).
Multiple functions of DNA polymerases.
  CRC Crit Rev Plant Sci, 26, 105-122.  
17441785 M.Salas, and M.Salas (2007).
40 years with bacteriophage ø29.
  Annu Rev Microbiol, 61, 1.  
17804463 M.Stahl, M.Retzlaff, M.Nassal, and J.Beck (2007).
Chaperone activation of the hepadnaviral reverse transcriptase for template RNA binding is established by the Hsp70 and stimulated by the Hsp90 system.
  Nucleic Acids Res, 35, 6124-6136.  
17913744 P.Pérez-Arnaiz, E.Longás, L.Villar, J.M.Lázaro, M.Salas, and M.de Vega (2007).
Involvement of phage phi29 DNA polymerase and terminal protein subdomains in conferring specificity during initiation of protein-primed DNA replication.
  Nucleic Acids Res, 35, 7061-7073.  
17071961 E.Longás, M.de Vega, J.M.Lázaro, and M.Salas (2006).
Functional characterization of highly processive protein-primed DNA polymerases from phages Nf and GA-1, endowed with a potent strand displacement capacity.
  Nucleic Acids Res, 34, 6051-6063.  
16900098 T.A.Steitz (2006).
Visualizing polynucleotide polymerase machines at work.
  EMBO J, 25, 3458-3468.  
17053784 Y.Xiang, M.C.Morais, A.J.Battisti, S.Grimes, P.J.Jardine, D.L.Anderson, and M.G.Rossmann (2006).
Structural changes of bacteriophage phi29 upon DNA packaging and release.
  EMBO J, 25, 5229-5239.  
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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