1VPR

Crystal structure of a luciferase domain from the dinoflagellate Lingulodinium polyedrum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a pH-regulated luciferase catalyzing the bioluminescent oxidation of an open tetrapyrrole

Schultz, L.W.Liu, L.Cegielski, M.Hastings, J.W.

(2005) Proc.Natl.Acad.Sci.USA 102: 1378-1383

  • DOI: 10.1073/pnas.0409335102

  • PubMed Abstract: 
  • The luciferase of Lingulodinium polyedrum, a marine bioluminescent dinoflagellate, consists of three similar but not identical domains in a single polypeptide. Each encodes an active luciferase that catalyzes the oxidation of a chlorophyll-derived op ...

    The luciferase of Lingulodinium polyedrum, a marine bioluminescent dinoflagellate, consists of three similar but not identical domains in a single polypeptide. Each encodes an active luciferase that catalyzes the oxidation of a chlorophyll-derived open tetrapyrrole (dinoflagellate luciferin) to produce blue light. These domains share no sequence similarity with any other in the GenBank database and no structural or motif similarity with any other luciferase. We report here the 1.8-A crystal structure of the third domain, D3, at pH 8, and a mechanism for its activity regulation by pH. D3 consists of two major structural elements: a beta-barrel pocket putatively for substrate binding and catalysis and a regulatory three-helix bundle. N-terminal histidine residues previously shown to regulate activity by pH are at the interface of the helices in the bundle. Molecular dynamics calculations indicate that, in response to changes in pH, these histidines could trigger a large molecular motion of the bundle, thereby exposing the active site to the substrate.


    Related Citations: 
    • Characterization and crystallization of active domains of a novel luciferase from a marine dinoflagellate
      Liu, L.,Im, H.,Cegielski, M.,LeMagueres, P.,Schultz, L.W.,Krause, K.L.,Hastings, J.W.
      (2003) Acta Crystallogr.,Sect.D 59: 761


    Organizational Affiliation

    Department of Structural Biology, Hauptman-Woodward Medical Research Institute, State University of New York, Buffalo, NY 14203, USA. schultz@hwi.buffalo.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
luciferase
A
374Lingulodinium polyedraMutation(s): 0 
EC: 1.13.12.18
Find proteins for O77206 (Lingulodinium polyedra)
Go to UniProtKB:  O77206
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.989α = 90.00
b = 63.955β = 90.00
c = 96.986γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SOLVEphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-08
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance