PDBsum entry 2pyj

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protein dna_rna ligands metals Protein-protein interface(s) links
Replication, transferase/DNA PDB id
Protein chains
567 a.a. *
EDO ×41
DGT ×2
_MN ×2
_MG ×2
Waters ×969
* Residue conservation analysis
PDB id:
Name: Replication, transferase/DNA
Title: Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)
Structure: 5'-d(gactgctta(doc)-3'. Chain: x, q, j. Engineered: yes. 5'-d(acacgtaagcagtc)-3'. Chain: y, r, k. Engineered: yes. DNA polymerase. Chain: a, b. Synonym: early protein gp2.
Source: Synthetic: yes. Bacillus phage phi29. Organism_taxid: 10756. Gene: 2, gp2. Expressed in: escherichia coli. Expression_system_taxid: 562
2.03Å     R-factor:   0.191     R-free:   0.234
Authors: A.J.Berman,S.Kamtekar,J.L.Goodman,J.M.Lazaro,M.De Vega, L.Blanco,M.Salas,T.A.Steitz
Key ref:
A.J.Berman et al. (2007). Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases. EMBO J, 26, 3494-3505. PubMed id: 17611604 DOI: 10.1038/sj.emboj.7601780
16-May-07     Release date:   17-Jul-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P03680  (DPOL_BPPH2) -  DNA polymerase
575 a.a.
567 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Deoxynucleoside triphosphate
Bound ligand (Het Group name = DGT)
matches with 62.00% similarity
+ DNA(n)
= diphosphate
+ DNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA replication   4 terms 
  Biochemical function     nucleotide binding     12 terms  


DOI no: 10.1038/sj.emboj.7601780 EMBO J 26:3494-3505 (2007)
PubMed id: 17611604  
Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases.
A.J.Berman, S.Kamtekar, J.L.Goodman, J.M.Lázaro, Vega, L.Blanco, M.Salas, T.A.Steitz.
Replicative DNA polymerases (DNAPs) move along template DNA in a processive manner. The structural basis of the mechanism of translocation has been better studied in the A-family of polymerases than in the B-family of replicative polymerases. To address this issue, we have determined the X-ray crystal structures of phi29 DNAP, a member of the protein-primed subgroup of the B-family of polymerases, complexed with primer-template DNA in the presence or absence of the incoming nucleoside triphosphate, the pre- and post-translocated states, respectively. Comparison of these structures reveals a mechanism of translocation that appears to be facilitated by the coordinated movement of two conserved tyrosine residues into the insertion site. This differs from the mechanism employed by the A-family polymerases, in which a conserved tyrosine moves into the templating and insertion sites during the translocation step. Polymerases from the two families also interact with downstream single-stranded template DNA in very different ways.
  Selected figure(s)  
Figure 3.
Figure 3 Water-mediated interactions maintain sequence nonspecific binding. The C:G base pair is from the ternary1 complex, and the A:T base pair is from the ternary2 complex. Red spheres are water molecules and black dashes are hydrogen bonds. Amino acids are colored by subdomain as in Kamtekar et al (2004).
Figure 4.
Figure 4 The I/YxGG/A motif. (A) The primer and template strands from the ternary complex are shown as yellow and gray sticks, respectively. The template strand and the residues of the I/YxGG/A motif are shown as spheres. (B) The two distinct populations of Y226 are shown in sticks based on a superposition of the palm subdomain. The residues are colored by crystal structure.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2007, 26, 3494-3505) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22785315 T.Nakamura, Y.Zhao, Y.Yamagata, Y.J.Hua, and W.Yang (2012).
Watching DNA polymerase η make a phosphodiester bond.
  Nature, 487, 196-201.
PDB codes: 4ecq 4ecr 4ecs 4ect 4ecu 4ecv 4ecw 4ecx 4ecy 4ecz 4ed0 4ed1 4ed2 4ed3 4ed6 4ed7 4ed8
21036870 D.A.Korona, K.G.Lecompte, and Z.F.Pursell (2011).
The high fidelity and unique error signature of human DNA polymerase epsilon.
  Nucleic Acids Res, 39, 1763-1773.  
20453866 B.A.Flusberg, D.R.Webster, J.H.Lee, K.J.Travers, E.C.Olivares, T.A.Clark, J.Korlach, and S.W.Turner (2010).
Direct detection of DNA methylation during single-molecule, real-time sequencing.
  Nat Methods, 7, 461-465.  
21071662 B.Pan, Y.Xiong, and T.A.Steitz (2010).
How the CCA-adding enzyme selects adenine over cytosine at position 76 of tRNA.
  Science, 330, 937-940.
PDB codes: 3ouy 3ov7 3ova 3ovb 3ovs
20123134 J.D.Pata (2010).
Structural diversity of the Y-family DNA polymerases.
  Biochim Biophys Acta, 1804, 1124-1135.  
20823261 Vega, J.M.Lázaro, M.Mencía, L.Blanco, and M.Salas (2010).
Improvement of φ29 DNA polymerase amplification performance by fusion of DNA binding motifs.
  Proc Natl Acad Sci U S A, 107, 16506-16511.  
19661923 B.Ibarra, Y.R.Chemla, S.Plyasunov, S.B.Smith, J.M.Lázaro, M.Salas, and C.Bustamante (2009).
Proofreading dynamics of a processive DNA polymerase.
  EMBO J, 28, 2794-2802.  
20064374 F.Wang, and W.Yang (2009).
Structural insight into translesion synthesis by DNA Pol II.
  Cell, 139, 1279-1289.
PDB codes: 3k57 3k58 3k59 3k5a 3k5l 3k5m 3k5n 3k5o 3maq
19033368 I.Rodríguez, J.M.Lázaro, M.Salas, and Vega (2009).
Involvement of the TPR2 subdomain movement in the activities of phi29 DNA polymerase.
  Nucleic Acids Res, 37, 193-203.  
19023044 J.Eid, A.Fehr, J.Gray, K.Luong, J.Lyle, G.Otto, P.Peluso, D.Rank, P.Baybayan, B.Bettman, A.Bibillo, K.Bjornson, B.Chaudhuri, F.Christians, R.Cicero, S.Clark, R.Dalal, A.Dewinter, J.Dixon, M.Foquet, A.Gaertner, P.Hardenbol, C.Heiner, K.Hester, D.Holden, G.Kearns, X.Kong, R.Kuse, Y.Lacroix, S.Lin, P.Lundquist, C.Ma, P.Marks, M.Maxham, D.Murphy, I.Park, T.Pham, M.Phillips, J.Roy, R.Sebra, G.Shen, J.Sorenson, A.Tomaney, K.Travers, M.Trulson, J.Vieceli, J.Wegener, D.Wu, A.Yang, D.Zaccarin, P.Zhao, F.Zhong, J.Korlach, and S.Turner (2009).
Real-time DNA sequencing from single polymerase molecules.
  Science, 323, 133-138.  
19375325 R.Johne, H.Müller, A.Rector, M.van Ranst, and H.Stevens (2009).
Rolling-circle amplification of viral DNA genomes using phi29 polymerase.
  Trends Microbiol, 17, 205-211.  
19300826 R.N.Veedu, B.Vester, and J.Wengel (2009).
Efficient enzymatic synthesis of LNA-modified DNA duplexes using KOD DNA polymerase.
  Org Biomol Chem, 7, 1404-1409.  
18263611 C.A.Howell, C.M.Kondratick, and M.T.Washington (2008).
Substitution of a residue contacting the triphosphate moiety of the incoming nucleotide increases the fidelity of yeast DNA polymerase zeta.
  Nucleic Acids Res, 36, 1731-1740.  
19011105 E.Longás, L.Villar, J.M.Lázaro, 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.  
19106298 R.J.Evans, D.R.Davies, J.M.Bullard, J.Christensen, L.S.Green, J.W.Guiles, J.D.Pata, W.K.Ribble, N.Janjic, and T.C.Jarvis (2008).
Structure of PolC reveals unique DNA binding and fidelity determinants.
  Proc Natl Acad Sci U S A, 105, 20695-20700.
PDB codes: 3f2b 3f2c 3f2d
18407502 S.Broyde, L.Wang, O.Rechkoblit, N.E.Geacintov, and D.J.Patel (2008).
Lesion processing: high-fidelity versus lesion-bypass DNA polymerases.
  Trends Biochem Sci, 33, 209-219.  
18287276 W.J.Allen, P.J.Rothwell, and G.Waksman (2008).
An intramolecular FRET system monitors fingers subdomain opening in Klentaq1.
  Protein Sci, 17, 401-408.  
17913744 P.Pérez-Arnaiz, E.Longás, L.Villar, J.M.Lázaro, M.Salas, and 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.  
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.