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PDBsum entry 2pyl
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Replication, transferase/DNA
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PDB id
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2pyl
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References listed in PDB file
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Key reference
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Title
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Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in b-Family polymerases.
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Authors
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A.J.Berman,
S.Kamtekar,
J.L.Goodman,
J.M.Lázaro,
M.De vega,
L.Blanco,
M.Salas,
T.A.Steitz.
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Ref.
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EMBO J, 2007,
26,
3494-3505.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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).
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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.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
EMBO J
(2007,
26,
3494-3505)
copyright 2007.
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