8CBB

Structure of homodimeric luciferase from Enhygromyxa salina


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 
    0.269 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

luxA Gene From Enhygromyxa salina Encodes a Functional Homodimeric Luciferase.

Yudenko, A.Bazhenov, S.V.Aleksenko, V.A.Goncharov, I.M.Semenov, O.Remeeva, A.Nazarenko, V.V.Kuznetsova, E.Fomin, V.V.Konopleva, M.N.Al Ebrahim, R.Sluchanko, N.N.Ryzhykau, Y.Semenov, Y.S.Kuklin, A.Manukhov, I.V.Gushchin, I.

(2024) Proteins 92: 1449-1458

  • DOI: https://doi.org/10.1002/prot.26739
  • Primary Citation of Related Structures:  
    8CBB

  • PubMed Abstract: 

    Several clades of luminescent bacteria are known currently. They all contain similar lux operons, which include the genes luxA and luxB encoding a heterodimeric luciferase. The aldehyde oxygenation reaction is presumed to be catalyzed primarily by the subunit LuxA, whereas LuxB is required for efficiency and stability of the complex. Recently, genomic analysis identified a subset of bacterial species with rearranged lux operons lacking luxB. Here, we show that the product of the luxA gene from the reduced luxACDE operon of Enhygromyxa salina is luminescent upon addition of aldehydes both in vivo in Escherichia coli and in vitro. Overall, EsLuxA is much less bright compared with luciferases from Aliivibrio fischeri (AfLuxAB) and Photorhabdus luminescens (PlLuxAB), and most active with medium-chain C4-C9 aldehydes. Crystal structure of EsLuxA determined at the resolution of 2.71 Å reveals a (β/α) 8 TIM-barrel fold, characteristic for other bacterial luciferases, and the protein preferentially forms a dimer in solution. The mobile loop residues 264-293, which form a β-hairpin or a coil in Vibrio harveyi LuxA, form α-helices in EsLuxA. Phylogenetic analysis shows EsLuxA and related proteins may be bacterial protoluciferases that arose prior to duplication of the luxA gene and its speciation to luxA and luxB in the previously described luminescent bacteria. Our work paves the way for the development of new bacterial luciferases that have an advantage of being encoded by a single gene.


  • Organizational Affiliation

    Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alkanal monooxygenase alpha chain
A, B, C, D
371Enhygromyxa salinaMutation(s): 0 
Gene Names: luxA
EC: 1.14.14.3
UniProt
Find proteins for A0A2S9XZH0 (Enhygromyxa salina)
Explore A0A2S9XZH0 
Go to UniProtKB:  A0A2S9XZH0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2S9XZH0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free:  0.269 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.821α = 88.72
b = 73.374β = 77.93
c = 93.972γ = 87.1
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Higher Education of the Russian FederationRussian Federation075-15-2021-1354

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2024-08-28
    Changes: Database references
  • Version 1.2: 2024-09-04
    Changes: Database references
  • Version 1.3: 2024-11-20
    Changes: Database references, Structure summary