 |
PDBsum entry 2jgu
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
E.C.2.7.7.7
- DNA-directed Dna polymerase.
|
|
|
|
|
|
|
Reaction:
|
|
DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
|
|
|
|
|
|
DNA(n)
|
+
|
2'-deoxyribonucleoside 5'-triphosphate
|
=
|
DNA(n+1)
|
+
|
diphosphate
|
|
|
|
|
|
|
|
|
|
|
|
|
Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
| |
|
|
Int J Biol Macromol
42:356-361
(2008)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
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.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
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
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
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.
|
|
Links
