PDBsum entry 2pd8

Circadian clock protein

PDB id: 2pd8

Contents

Protein chains

148 a.a. *

140 a.a. *

Ligands

FAD ×2

Waters ×373

* Residue conservation analysis

PDB id:

2pd8

Name:

Circadian clock protein

Title:

1.8 angstrom crystal structure of the cys71ser mutant of vivid

Structure:

Vivid pas protein vvd. Chain: a, b. Fragment: residues 37-184. Synonym: hypothetical protein ncu03967.1. Engineered: yes. Mutation: yes

Source:

Neurospora crassa. Organism_taxid: 5141. Gene: vvd, g17a4.050. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.80Å R-factor: 0.262 R-free: 0.284

Authors:

B.D.Zoltowski,B.R.Crane,A.M.Bilwes

Key ref:

B.D.Zoltowski et al. (2007). Conformational switching in the fungal light sensor Vivid. Science, 316, 1054-1057. PubMed id: 17510367 DOI: 10.1126/science.1137128

Date:

31-Mar-07 Release date: 05-Jun-07

Protein chain

Q9C3Y6  (Q9C3Y6_NEUCS) -  Vivid PAS protein VVD from Neurospora crassa

Seq: 186 a.a.

Struc: 148 a.a.*

Protein chain

Q9C3Y6  (Q9C3Y6_NEUCS) -  Vivid PAS protein VVD from Neurospora crassa

Seq: 186 a.a.

Struc: 140 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1126/science.1137128

Science 316:1054-1057 (2007)

PubMed id: 17510367

Conformational switching in the fungal light sensor Vivid.

B.D.Zoltowski, C.Schwerdtfeger, J.Widom, J.J.Loros, A.M.Bilwes, J.C.Dunlap, B.R.Crane.

ABSTRACT

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).

Selected figure(s)

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.

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.

The above figures are reprinted by permission from the AAAs: Science (2007, 316, 1054-1057) copyright 2007.

Figures were selected by an automated process.