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PDBsum entry 3hjk

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protein ligands Protein-protein interface(s) links
Signaling protein PDB id
3hjk
Jmol
Contents
Protein chains
150 a.a. *
140 a.a. *
Ligands
FAD ×2
Waters ×312
* Residue conservation analysis
PDB id:
3hjk
Name: Signaling protein
Title: 2.0 angstrom structure of the ile74val variant of vivid (vvd).
Structure: Vivid pas protein vvd. Chain: a, b. Engineered: yes. Mutation: yes
Source: Neurospora crassa. Organism_taxid: 5141. Gene: g17a4.050, vivid, vvd. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.244     R-free:   0.261
Authors: B.D.Zoltowski,B.J.Vaccaro,B.R.Crane
Key ref:
B.D.Zoltowski et al. (2009). Mechanism-based tuning of a LOV domain photoreceptor. Nat Chem Biol, 5, 827-834. PubMed id: 19718042 DOI: 10.1038/nchembio.210
Date:
21-May-09     Release date:   29-Sep-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9C3Y6  (Q9C3Y6_NEUCS) -  Vivid PAS protein VVD
Seq:
Struc:
186 a.a.
150 a.a.*
Protein chain
Pfam   ArchSchema ?
Q9C3Y6  (Q9C3Y6_NEUCS) -  Vivid PAS protein VVD
Seq:
Struc:
186 a.a.
140 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     signal transduction   1 term 
  Biochemical function     signal transducer activity     1 term  

 

 
DOI no: 10.1038/nchembio.210 Nat Chem Biol 5:827-834 (2009)
PubMed id: 19718042  
 
 
Mechanism-based tuning of a LOV domain photoreceptor.
B.D.Zoltowski, B.Vaccaro, B.R.Crane.
 
  ABSTRACT  
 
Phototropin-like LOV domains form a cysteinyl-flavin adduct in response to blue light but show considerable variation in output signal and the lifetime of the photo-adduct signaling state. Mechanistic studies of the slow-cycling fungal LOV photoreceptor Vivid (VVD) reveal the importance of reactive cysteine conformation, flavin electronic environment and solvent accessibility for adduct scission and thermal reversion. Proton inventory, pH effects, base catalysis and structural studies implicate flavin N(5) deprotonation as rate-determining for recovery. Substitutions of active site residues Ile74, Ile85, Met135 and Met165 alter photoadduct lifetimes by over four orders of magnitude in VVD, and similar changes in other LOV proteins show analogous effects. Adduct state decay rates also correlate with changes in conformational and oligomeric properties of the protein necessary for signaling. These findings link natural sequence variation of LOV domains to function and provide a means to design broadly reactive light-sensitive probes.
 
  Selected figure(s)  
 
Figure 1.
(a) Structure of VVD-36 with the PAS core (blue), N-terminal cap (yellow) and FAD binding loop (red). (b) Thermal reversion mechanism for phototropin-like LOV domains. Adduct scission is base (B) catalyzed and may involve solvent, a conserved glutamine residue that hydrogen bonds to N5, the active site cysteine or exogenous compounds such as imidazole.
Figure 5.
(a–c) Electron density for alternate conformations of Cys108 in VVD-36 (a), I74V (b) and I74V I85V (c). 2F[o] − F[c] maps are contoured at 1σ (cyan) and 2σ (purple); F[o] − F[c] maps are contoured at 3σ (green). VVD-36 has mostly conf1; I74V I85V only conf2, and I74V has both. (d) SEC elution profile of I74V I85V. I74V I85V (green) elutes intermediate of the light-adapted (red) and dark-adapted (black) states of VVD-36 on a Superdex 75 26/60 preparative column.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Chem Biol (2009, 5, 827-834) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21352235 A.Losi, and W.Gärtner (2011).
Old chromophores, new photoactivation paradigms, trendy applications: flavins in blue light-sensing photoreceptors.
  Photochem Photobiol, 87, 491-510.  
21028987 D.F.Becker, W.Zhu, and M.A.Moxley (2011).
Flavin redox switching of protein functions.
  Antioxid Redox Signal, 14, 1079-1091.  
21261629 I.H.van Stokkum, M.Gauden, S.Crosson, R.van Grondelle, K.Moffat, and J.T.Kennis (2011).
The primary photophysics of the Avena sativa phototropin 1 LOV2 domain observed with time-resolved emission spectroscopy.
  Photochem Photobiol, 87, 534-541.  
21187431 N.Ozturk, C.P.Selby, Y.Annayev, D.Zhong, and A.Sancar (2011).
Reaction mechanism of Drosophila cryptochrome.
  Proc Natl Acad Sci U S A, 108, 516-521.  
21336931 T.Drepper, U.Krauss, S.Meyer Zu Berstenhorst, J.Pietruszka, and K.E.Jaeger (2011).
Lights on and action! Controlling microbial gene expression by light.
  Appl Microbiol Biotechnol, 90, 23-40.  
21305623 U.Krauss, T.Drepper, and K.E.Jaeger (2011).
Enlightened enzymes: strategies to create novel photoresponsive proteins.
  Chemistry, 17, 2552-2560.  
20835487 A.Möglich, and K.Moffat (2010).
Engineered photoreceptors as novel optogenetic tools.
  Photochem Photobiol Sci, 9, 1286-1300.  
20813262 E.Malzahn, S.Ciprianidis, K.Káldi, T.Schafmeier, and M.Brunner (2010).
Photoadaptation in Neurospora by competitive interaction of activating and inhibitory LOV domains.
  Cell, 142, 762-772.  
20676078 K.M.Hahn, and B.Kuhlman (2010).
Hold me tightly LOV.
  Nat Methods, 7, 595, 597.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.