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PDBsum entry 2vtb
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References listed in PDB file
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Key reference
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Title
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Recognition and repair of uv lesions in loop structures of duplex DNA by dash-Type cryptochrome.
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Authors
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R.Pokorny,
T.Klar,
U.Hennecke,
T.Carell,
A.Batschauer,
L.O.Essen.
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Ref.
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Proc Natl Acad Sci U S A, 2008,
105,
21023-21027.
[DOI no: ]
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PubMed id
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Abstract
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DNA photolyases and cryptochromes (cry) form a family of flavoproteins that use
light energy in the blue/UV-A region for the repair of UV-induced DNA lesions or
for signaling, respectively. Very recently, it was shown that members of the
DASH cryptochrome subclade repair specifically cyclobutane pyrimidine dimers
(CPDs) in UV-damaged single-stranded DNA. Here, we report the crystal structure
of Arabidopsis cryptochrome 3 with an in-situ-repaired CPD substrate in
single-stranded DNA. The structure shows a binding mode similar to that of
conventional DNA photolyases. Furthermore, CPD lesions in double-stranded DNA
are bound and repaired with similar efficiency as in single-stranded DNA if the
CPD lesion is present in a loop structure. Together, these data reveal that DASH
cryptochromes catalyze light-driven DNA repair like conventional photolyases but
lack an efficient flipping mechanism for interaction with CPD lesions within
duplex DNA.
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Figure 3.
Isoelectric surface potential of A. t. cry3 bound to the
single-stranded pentameric DNA containing a CPD analog. (A) Top
and side (Inset) views. (B and C) Hydration and electrostatics
of the active site in the substrate-bound state of cry3. The
black arrows in C indicate the water molecules intruded into the
active site because of replacement of a tryptophan conserved in
class I CPD photolyases by Y434.
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Figure 4.
Binding of cry3 to DNA probes containing a single T<>T dimer
in the central position. (A) Sequences and structures of probes.
The T<>T dimer is positioned within the VspI recognition site
(boxed in probe 1). Probe 1 forms a perfect duplex. In probes 2
and 3, the 5′ and 3′ thymines, respectively, of the T<>T
dimer are not hydrogen bonded to the complementary strand. In
probe 3, only one hydrogen bond is formed between the 5′
thymine of the T<>T dimer and the complementary adenine (23). In
probes 4–8, the T<>T lesion is positioned in the center of
loop structures with 2–10 base pairs. Hydrogen bonds between
complementary bases are shown as dashed lines. The upper strand
(50 nt) was labeled at the 5′ position with IRDye700 (MWG
Biotech AG) (marked with asterisk). (B and C) EMSA showing cry3
binding to probes with (B) or without (C) the central T<>T
dimer. Probes shown in A and the single-stranded control (probe
9) were mixed with cry3 (+) or with the same aliquot of buffer
(−). Arrows indicate the positions of shifted bands.
Representative gels from 2 independent experiments are shown.
(D) Quantitative binding data. Mean values and standard errors
of the 2 independent experiments are shown.
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Secondary reference #1
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Title
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Cryptochrome 3 from arabidopsis thaliana: structural and functional analysis of its complex with a folate light antenna.
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Authors
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T.Klar,
R.Pokorny,
J.Moldt,
A.Batschauer,
L.O.Essen.
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Ref.
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J Mol Biol, 2007,
366,
954-964.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. (a) Overall structure of Arabidopsis cry3. The
N-terminal antenna domain is shown in green, the FAD-binding
domain in grey. The dimeric organisation is shown on the left.
(b) Structural comparison of A. thaliana cry3 with CryDASH from
S. sp. (magenta, 1NP7), A. thaliana cry1 (orange, 1U3D), E. coli
DNA photolyase (blue, 1DNP) and A. nidulans photolyase (cyan,
1TEZ). The MTHF (orange), FAD (yellow) and 8-HDF chromophores
(blue, from the A. nidulans DNA photolyase) are shown with their
molecular surfaces. The N-terminal extension that is a unique
feature of cry3 is coloured in red. (c) Chromophore arrangement
in the E. coli DNA photolyase. This Figure and Figures 2, 3, 4
were prepared by PyMOL [http://www.pymol.org].
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Figure 4.
Figure 4. The MTHF binding site of A. thaliana cry3. Stereo
diagrams showing the MTHF binding site of (a) A. thaliana cry3
and (c) E. coli DNA photolyase. (b) Schematic diagram of
MTHF–cry3 interactions.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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