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References listed in PDB file
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Key reference
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Title
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A closed conformation for the pol lambda catalytic cycle.
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Authors
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M.Garcia-Diaz,
K.Bebenek,
J.M.Krahn,
T.A.Kunkel,
L.C.Pedersen.
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Ref.
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Nat Struct Mol Biol, 2005,
12,
97-98.
[DOI no: ]
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PubMed id
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Abstract
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Pol lambda is a family X member believed to fill short gaps during DNA repair.
Here we report crystal structures of Pol lambda representing three steps in
filling a single-nucleotide gap. These structures indicate that, unlike other
DNA polymerases, Pol lambda does not undergo large subdomain movements during
catalysis, and they provide a clear characterization of the geometry and
stereochemistry of the in-line nucleotidyl transfer reaction.
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Figure 1.
Figure 1. Superimposition of the Pol  structures.
(a) The C  traces
of the binary (dark gray), nick ternary (green) and precatalytic
ternary (orange) structures reveal two differences. One involves
 -strand
8 (ref. 10) (labeled A). The second involves -strands
3 and 4 (B; see text). Black lines indicate the span of the
different subdomains: 8 kDa domain (8), fingers (F), palm (P)
and thumb (T). (b) DNA shift upon dNTP binding. The DNA and part
of the palm subdomain is shown for the binary (blue) and
precatalytic ternary complex (yellow-brown). Hydrogen bonds,
dashed lines; Mg2+ ion observed in the structure of the ternary
complex, green.
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Figure 2.
Figure 2. Conformational changes and nucleotidyl transfer
catalysis. (a) Stereo representation of an overlay of the Pol
 active
site in the binary (gray) and precatalytic ternary (brown)
complex structures, focusing on the side chain movements
observed upon dNTP binding. Hydrogen bonds, dashed lines. (b)
Stereo view of the postcatalytic ternary complex. The two last
bases of the primer strand and the catalytic carboxylates are
shown, together with the pyrophosphate molecule. An overlay of
the equivalent atoms in the structure of the precatalytic
ternary complex is transparent. The line of transfer, dashed
line. The 3' O that was the acceptor in the reaction (3'O[N]),
the bridging oxygen of the leaving group (O[L]) and the phosphate
(P )
are labeled.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2005,
12,
97-98)
copyright 2005.
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Secondary reference #1
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Title
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A structural solution for the DNA polymerase lambda-Dependent repair of DNA gaps with minimal homology.
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Authors
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M.Garcia-Diaz,
K.Bebenek,
J.M.Krahn,
L.Blanco,
T.A.Kunkel,
L.C.Pedersen.
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Ref.
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Mol Cell, 2004,
13,
561-572.
[DOI no: ]
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PubMed id
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Figure 4.
Figure 4. Superimposition of Pol λ with the Open and
Closed Conformations of Pol βSuperimposition of the α carbon
trace of human Pol λ (red) with the structures of human Pol β
in an open (1BPX; yellow) and closed (1BPY; blue) conformation.
The roman numerals refer to different regions of the Pol λ
structure as indicated in the text. The rms deviation was 1.4
Å for 112 C-α atoms for 1BPX and 1.4 Å for 113 C-α
atoms for 1BPY.
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Figure 7.
Figure 7. Biological Implications of the Pol λ
Structure(A) Stereo view of an overlay of the active site of Pol
λ with that of Pol β in a closed conformation (1BPY). The DNA
corresponds to the Pol λ structure, while the incoming ddCTP
(green) and metal ions (gray balls) correspond to Pol β 1BPY.
Relevant residues are shown in red (Pol λ) and blue (Pol β).
The template strand is gray and the primer terminus is
yellow.(B) Electrostatic surface potential of Pol λ and Pol β.
The DNA for each of the structures is shown in gray (template)
and yellow (primer and downstream primer). The potential ranges
from −8 kT/e (red) to 8 kT/e (blue).
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #2
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Title
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Dna polymerase lambda, A novel DNA repair enzyme in human cells.
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Authors
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M.García-Díaz,
K.Bebenek,
R.Sabariegos,
O.Domínguez,
J.Rodríguez,
T.Kirchhoff,
E.García-Palomero,
A.J.Picher,
R.Juárez,
J.F.Ruiz,
T.A.Kunkel,
L.Blanco.
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Ref.
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J Biol Chem, 2002,
277,
13184-13191.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Multiple amino acid alignment of human and mouse
orthologs of pol  with
human pol  . Numbers
indicate the amino acid position relative to the N terminus of
each DNA polymerase. Invariant residues in the three enzymes
aligned are indicated in white letters over a black background.
Other amino acid identities with respect to human pol sequence
are indicated in bold letters. Amino acids 36-126 (human pol
) and
35-125 (murine pol (20)) are
predicted to form a BRCT domain (light gray). Amino acids
241-575 (human pol ) and
239-573 (murine pol (20))
form a conserved -core,
including an 8-kDa domain (gray) and a 31-kDa polymerization
domain (dark gray). The 23 amino acid residues that are
invariant among all family X DNA polymerases (34) are indicated
by an asterisk at the top of the alignment.
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Figure 5.
Fig. 5. Structural basis for nucleotide binding by human
pol . The
nucleotide binding pocket of human pol (A) is
compared with the putative (modeled) nucleotide binding pocket
of human pol (B). The
incoming ddCTP (red) is shown, hydrogen bonded to its templating
base (light yellow). Relevant residues are shown (ball and
stick), and their position relative to the N terminus of the
protein is indicated. One of the most striking differences
between the pol and pol
dNTP
binding site is the nonconservation of pol residue
Asp276 (green), which plays a direct role in dNTP binding and
selectivity (for details, see "Discussion"). A model structure
of the whole -core of
human pol , with the
exception of  -helix A,
was generated with the program Swiss Model
(www.expasy.ch/swissmod/swiss-model.html). The figure was made
with Swiss PDB Viewer ((42) www.expasy.ch/spdbv/) and rendered
with POV Ray (www.povray.org).
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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Secondary reference #3
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Title
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The frameshift infidelity of human DNA polymerase lambda. Implications for function.
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Authors
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K.Bebenek,
M.Garcia-Diaz,
L.Blanco,
T.A.Kunkel.
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Ref.
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J Biol Chem, 2003,
278,
34685-34690.
[DOI no: ]
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PubMed id
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Figure 1.
FIG. 1. Single base error spectrum of human DNA Pol  . The
407 template nucleotides within the single-strand gap of the
M13mp2 substrate DNA are shown as 5 lines of the template
sequence, with nucleotide +1 as the first transcribed nucleotide
of the LacZ  -complementation
region. Base substitutions are indicated by letters below the
line of the target sequence. Deletion of a base is depicted by
an open triangle above the line of the sequence, whereas
addition of a base is indicated below the line of the sequence
by "  " immediately above
the added base. The arrow indicates the direction of synthesis.
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Figure 4.
FIG. 4. The binding pocket for the nascent base pair at the
active site of Pol  . Pol residues
that interact with the templating base (colored green) and the
incoming nucleotide (colored yellow) that are conserved in Pol
are colored brown.
Those residues that are not conserved are depicted in cyan, dark
blue, and red for Ala-185, Lys-280, and Asp-276, respectively.
The figure was created based on the structure of Pol in
ternary complex with gapped DNA and the incoming ddCTP (Protein
Data Bank accession number 1BPY [PDB]
) using Molscript (57), GRASP (58), and Raster3D (59).
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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Secondary reference #4
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Title
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Identification of an intrinsic 5'-Deoxyribose-5-Phosphate lyase activity in human DNA polymerase lambda: a possible role in base excision repair.
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Authors
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M.García-Díaz,
K.Bebenek,
T.A.Kunkel,
L.Blanco.
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Ref.
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J Biol Chem, 2001,
276,
34659-34663.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. A, multiple amino acid alignment of the 8-kDa
domain of human Pol with the
other human family X DNA polymerases. Residues described to be
relevant to the 8-kDa domain function of Pol (His34,
Lys35, Tyr39, Lys60, Lys68, Glu71, Lys72, Glu75, and Lys84) are
indicated in white letters over a black background. The position
of Lys310 (Pol residue
Lys72) is indicated with an asterisk. Invariant (bold type) and
conservative substitutions referred to Pol residues
are boxed in dark and light gray, respectively. The arrow
indicates the position of proteolytic cleavage for Pol . B,
schematic representation of a dRP lyase reaction. A 34-mer
double-stranded oligonucleotide containing an uracil residue at
position 16 in one strand is treated with hUDG and hAPE to
release a dRP-containing substrate. This dRP moiety will be
cleaved by dRP lyase activity. C, autoradiogram illustrating Pol
dRP lyase
activity. 10-Min reactions were performed as described under
"Experimental Procedures," using 50 nM Pol , 80 nM
(wild-type) or 100 nM (K310A mutant) Pol . Asterisk
indicates the use of a reduced AP substrate.
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Figure 3.
Fig. 3. In vitro reconstitution of single-nucleotide BER.
A, schematic representation of a reconstituted BER reaction,
indicating the different products formed. B, autoradiogram
illustrating the products observed during an in vitro BER
reaction with Pol or Pol .
Reactions were carried out as described under "Experimental
Procedures."
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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