long-chain alkane monooxygenase (LadA) in complex with coenzyme FMN

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.196 

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Crystal structure of long-chain alkane monooxygenase (LadA) in complex with coenzyme FMN: unveiling the long-chain alkane hydroxylase

Li, L.Liu, X.Yang, W.Xu, F.Wang, W.Feng, L.Bartlam, M.Wang, L.Rao, Z.

(2008) J Mol Biol 376: 453-465

  • DOI: https://doi.org/10.1016/j.jmb.2007.11.069
  • Primary Citation of Related Structures:  
    3B9N, 3B9O

  • PubMed Abstract: 

    LadA, a long-chain alkane monooxygenase, utilizes a terminal oxidation pathway for the conversion of long-chain alkanes (up to at least C(36)) to corresponding primary alcohols in thermophilic bacillus Geobacillus thermodenitrificans NG80-2. Here, we report the first structure of the long-chain alkane hydroxylase, LadA, and its complex with the flavin mononucleotide (FMN) coenzyme. LadA is characterized as a new member of the SsuD subfamily of the bacterial luciferase family via a surprising structural relationship. The LadA:FMN binary complex structure and a LadA:FMN:alkane model reveal a hydrophobic cavity that has dual roles: to provide a hydrogen-bond donor (His138) for catalysis and to create a solvent-free environment in which to stabilize the C4a-hydroperoxyflavin intermediate. Consequently, LadA should catalyze the conversion of long-chain alkanes via the acknowledged flavoprotein monooxygenase mechanism. This finding suggests that the ability of LadA to catalyze the degradation of long-chain alkanes is determined by the binding mode of the long-chain alkane substrates. The LadA structure opens a rational perspective to explore and alter the substrate binding site of LadA, with potential biotechnological applications in areas such as petroleum exploration and treatment of environmental oil pollution.

  • Organizational Affiliation

    Tsinghua-Nankai-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alkane monooxygenase
A, B
440Geobacillus thermodenitrificansMutation(s): 0 
Gene Names: ladA
EC: 1.14.15 (PDB Primary Data), (UniProt)
Find proteins for A4IU28 (Geobacillus thermodenitrificans (strain NG80-2))
Explore A4IU28 
Go to UniProtKB:  A4IU28
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4IU28
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.196 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.951α = 90
b = 76.951β = 90
c = 323.467γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description