PDBsum entry 2jgu

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protein metals links
Transferase PDB id
Protein chain
712 a.a. *
_MN ×2
Waters ×31
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of DNA-directed DNA polymerase
Structure: DNA polymerase. Chain: a. Synonym: pfu polymerase, DNA polymerase pfu. Engineered: yes
Source: Pyrococcus furiosus. Organism_taxid: 2261. Expressed in: escherichia coli. Expression_system_taxid: 511693.
2.60Å     R-factor:   0.274     R-free:   0.271
Authors: D.U.Kim,H.S.Cho
Key ref: S.W.Kim et al. (2008). Crystal structure of Pfu, the high fidelity DNA polymerase from Pyrococcus furiosus. Int J Biol Macromol, 42, 356-361. PubMed id: 18355915 DOI: 10.1016/j.ijbiomac.2008.01.010
15-Feb-07     Release date:   22-Apr-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P61875  (DPOL_PYRFU) -  DNA polymerase
775 a.a.
712 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 10 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
+ 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 biosynthetic process   3 terms 
  Biochemical function     nucleotide binding     10 terms  


DOI no: 10.1016/j.ijbiomac.2008.01.010 Int J Biol Macromol 42:356-361 (2008)
PubMed id: 18355915  
Crystal structure of Pfu, the high fidelity DNA polymerase from Pyrococcus furiosus.
S.W.Kim, D.U.Kim, J.K.Kim, L.W.Kang, H.S.Cho.
We have determined a 2.6A resolution crystal structure of Pfu DNA polymerase, the most commonly used high fidelity PCR enzyme, from Pyrococcus furiosus. Although the structures of Pfu and KOD1 are highly similar, the structure of Pfu elucidates the electron density of the interface between the exonuclease and thumb domains, which has not been previously observed in the KOD1 structure. The interaction of these two domains is known to coordinate the proofreading and polymerization activity of DNA polymerases, especially via H147 that is present within the loop (residues 144-158) of the exonuclease domain. In our structure of Pfu, however, E148 rather than H147 is located at better position to interact with the thumb domain. In addition, the structural analysis of Pfu and KOD1 shows that both the Y-GG/A and beta-hairpin motifs of Pfu are found to differ with that of KOD1, and may explain differences in processivity. This information enables us to better understand the mechanisms of polymerization and proofreading of DNA polymerases.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21062827 C.J.Hansen, L.Wu, J.D.Fox, B.Arezi, and H.H.Hogrefe (2011).
Engineered split in Pfu DNA polymerase fingers domain improves incorporation of nucleotide gamma-phosphate derivative.
  Nucleic Acids Res, 39, 1801-1810.  
21146395 E.S.Kim, B.J.Hong, C.W.Park, Y.Kim, J.W.Park, and K.Y.Choi (2011).
Effects of lateral spacing on enzymatic on-chip DNA polymerization.
  Biosens Bioelectron, 26, 2566-2573.  
21245343 K.Mayanagi, S.Kiyonari, H.Nishida, M.Saito, D.Kohda, Y.Ishino, T.Shirai, and K.Morikawa (2011).
Architecture of the DNA polymerase B-proliferating cell nuclear antigen (PCNA)-DNA ternary complex.
  Proc Natl Acad Sci U S A, 108, 1845-1849.  
20601675 K.Szczepanowska, and F.Foury (2010).
A cluster of pathogenic mutations in the 3'-5' exonuclease domain of DNA polymerase gamma defines a novel module coupling DNA synthesis and degradation.
  Hum Mol Genet, 19, 3516-3529.  
19934045 H.Nishida, K.Mayanagi, S.Kiyonari, Y.Sato, T.Oyama, Y.Ishino, and K.Morikawa (2009).
Structural determinant for switching between the polymerase and exonuclease modes in the PCNA-replicative DNA polymerase complex.
  Proc Natl Acad Sci U S A, 106, 20693-20698.  
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