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PDBsum entry 2pd8
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Circadian clock protein
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PDB id
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2pd8
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References listed in PDB file
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Key reference
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Title
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Conformational switching in the fungal light sensor vivid.
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Authors
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B.D.Zoltowski,
C.Schwerdtfeger,
J.Widom,
J.J.Loros,
A.M.Bilwes,
J.C.Dunlap,
B.R.Crane.
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Ref.
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Science, 2007,
316,
1054-1057.
[DOI no: ]
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PubMed id
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Abstract
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The Neurospora crassa photoreceptor Vivid tunes blue-light responses and
modulates gating of the circadian clock. Crystal structures of dark-state and
light-state Vivid reveal a light, oxygen, or voltage Per-Arnt-Sim domain with an
unusual N-terminal cap region and a loop insertion that accommodates the flavin
cofactor. Photoinduced formation of a cystein-flavin adduct drives flavin
protonation to induce an N-terminal conformational change. A cysteine-to-serine
substitution remote from the flavin adenine dinucleotide binding site decouples
conformational switching from the flavin photocycle and prevents Vivid from
sending signals in Neurospora. Key elements of this activation mechanism are
conserved by other photosensors such as White Collar-1, ZEITLUPE, ENVOY, and
flavin-binding, kelch repeat, F-BOX 1 (FKF1).
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Figure 1.
Fig. 1. VVD structure. (A) Crystallographic dimer of VVD-36,
including the PAS core (blue), N-terminal cap (yellow), and FAD
insertion loop (red). The N terminus, resolved only in the left
molecule, projects toward the solvent-exposed FAD adenosine
moiety (orange). (B) Superposition of the PAS domains of VVD
(green), PYP (magenta), Drosophila PER (red), and AsLOV2 domain
(blue). All proteins share a structurally conserved PAS ß
scaffold (yellow) and helical regions (gray) that pack with a
variable helical element possibly involved in signal
transduction. (C) Photocycle of VVD-36 at 25°C. Blue-light
illumination of VVD forms a photoadduct between Cys^108 and the
C4a position of the flavin ring (inset). Adduct formation
bleaches the flavin absorption bands at 428, 450, and 478 nm and
produces a single peak at 390 nm. Recovery proceeds with t[1/2]
= 10^4 s and three isosbestic points at 330, 385, and 413 nm.
Spectra are displayed at 3000 s increments.
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Figure 2.
Fig. 2. The VVD light state in crystals. (A) Superposition of
VVD (yellow) and Adiantum phy3-LOV2 (1G28, blue-gray) active
centers show differences in residue composition beneath the
flavin [1.5  (aqua) and 3.0
(purple), 2F[obs]
– F[calc] electron density]. An alternate conformation of
Cys^108 contacts conserved Cys^76 [3.0 (green), F[obs]
– F[calc] electron density]. (B) Structural differences in the
light state of VVD. Difference electron density reveals covalent
bond formation between Cys^108 and flavin C4a and flipping of
the Gln^182 amide in response to N5 protonation. F[obs] –
F[calc] electron density [2.0 (aqua), 3.0 (blue), –2.0
(orange), and
–3.0 (red)], with
F[calc] calculated from a model refined with 100% of the
dark-state conformation. (C) Expanded view of the structural
changes propagating from Gln^182 to a  and bß in
the VVD-36 light state. Pro^66 undergoes the largest shift (2.0
Å) in the light state (yellow) versus the dark state
(orange). Hydrogen bonds (dashed lines) are shown for d < 3.2
Å; except for Cys^71-to-Asp^68 amide, where d = 3.9
Å. Other key contacts are shown in blue. (D) The hinge
region between the PAS core and bß. In the light state,
Gln^182 rotates to improve interactions between the Gln^182
amide and the Ala^72 carbonyl, Cys^71 swivels to hydrogen-bond
with the Asp^68 amide nitrogen, and bß shifts 2 Å.
F[obs] – F[calc] omit electron density [1.5 (aqua) and 3.0
(purple)]
calculated with bß absent from the model.
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The above figures are
reprinted
by permission from the AAAs:
Science
(2007,
316,
1054-1057)
copyright 2007.
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