4KUO | pdb_00004kuo

A superfast recovering full-length LOV protein from the marine phototrophic bacterium Dinoroseobacter shibae (Photoexcited state)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.182 (Depositor), 0.181 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structure and function of a short LOV protein from the marine phototrophic bacterium Dinoroseobacter shibae.

Endres, S.Granzin, J.Circolone, F.Stadler, A.Krauss, U.Drepper, T.Svensson, V.Knieps-Grunhagen, E.Wirtz, A.Cousin, A.Tielen, P.Willbold, D.Jaeger, K.E.Batra-Safferling, R.

(2015) BMC Microbiol 15: 30-30

  • DOI: https://doi.org/10.1186/s12866-015-0365-0
  • Primary Citation Related Structures: 
    4KUK, 4KUO

  • PubMed Abstract: 

    Light, oxygen, voltage (LOV) domains are widely distributed in plants, algae, fungi, bacteria, and represent the photo-responsive domains of various blue-light photoreceptor proteins. Their photocycle involves the blue-light triggered adduct formation between the C(4a) atom of a non-covalently bound flavin chromophore and the sulfur atom of a conserved cysteine in the LOV sensor domain. LOV proteins show considerable variation in the structure of N- and C-terminal elements which flank the LOV core domain, as well as in the lifetime of the adduct state. Here, we report the photochemical, structural and functional characterization of DsLOV, a LOV protein from the photoheterotrophic marine α-proteobacterium Dinoroseobacter shibae which exhibits an average adduct state lifetime of 9.6 s at 20°C, and thus represents the fastest reverting bacterial LOV protein reported so far. Mutational analysis in D. shibae revealed a unique role of DsLOV in controlling the induction of photopigment synthesis in the absence of blue-light. The dark state crystal structure of DsLOV determined at 1.5 Å resolution reveals a conserved core domain with an extended N-terminal cap. The dimer interface in the crystal structure forms a unique network of hydrogen bonds involving residues of the N-terminus and the β-scaffold of the core domain. The structure of photoexcited DsLOV suggests increased flexibility in the N-cap region and a significant shift in the Cα backbone of β strands in the N- and C-terminal ends of the LOV core domain. The results presented here cover the characterization of the unusual short LOV protein DsLOV from Dinoroseobacter shibae including its regulatory function, extremely fast dark recovery and an N-terminus mediated dimer interface. Due to its unique photophysical, structural and regulatory properties, DsLOV might thus serve as an alternative model system for studying light perception by LOV proteins and physiological responses in bacteria.


  • Organizational Affiliation
    • Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, D-52425, Jülich, Germany. s.endres@fz-juelich.de.

Macromolecule Content 

  • Total Structure Weight: 17.24 kDa 
  • Atom Count: 1,015 
  • Modeled Residue Count: 115 
  • Deposited Residue Count: 146 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
blue-light photoreceptor146Dinoroseobacter shibae DFL 12 = DSM 16493Mutation(s): 0 
Gene Names: Dshi_2006
UniProt
Find proteins for A8LP63 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12))
Explore A8LP63 
Go to UniProtKB:  A8LP63
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8LP63
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RBF

Query on RBF



Download:Ideal Coordinates CCD File
B [auth A]RIBOFLAVIN
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.182 (Depositor), 0.181 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.78α = 90
b = 30.936β = 113.09
c = 49.538γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2015-03-04
    Changes: Database references
  • Version 1.2: 2015-04-01
    Changes: Database references
  • Version 1.3: 2015-04-29
    Changes: Database references
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description