9L10 | pdb_00009l10

Crystal structure of flavin reductase (StnC) complexed with FMN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 
    0.295 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

Starting Model: in silico
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Literature

A new family of StnC-like pseudo-FMN-preferred reductase components in two-component flavoprotein monooxygenases.

Xie, X.Wang, X.Yang, X.Ji, S.Ouyang, X.Zhou, Z.Xiao, Z.Guo, W.Liang, R.Huang, T.Deng, Z.Zhao, Y.L.Lin, S.

(2025) Int J Biol Macromol 328: 147543-147543

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.147543
  • Primary Citation of Related Structures:  
    9L10, 9L11

  • PubMed Abstract: 

    The reductase components of two-component flavoprotein monooxygenases (FPMOs) can reduce flavin mononucleotide (FMN) or flavin adenine dinucleotide (FAD) for their monooxygenase partners. Typically, the type of flavin cofactor bound by a flavoenzyme dictates the cofactor applied in its catalytic reactions. Here, we report the discovery of StnC, a previously unknown reductase family member involved in the biosynthesis of streptonigrin, a potent antimicrobial and antitumor compound. StnC exhibits a paradoxical performance in binding ability and catalytic activity toward flavins. Specifically, it binds FMN 147-fold stronger than FAD, but reduces FAD six times faster than FMN, enabling it to supply reduced FAD to its FAD-preferred monooxygenase partner StnD efficiently. Crystallographic, computational, and structural comparative analyses identified key residues and distinct structural features in StnC-like reductases, including extended clamp-like loops, that enable tight FMN binding and efficient FAD reduction. These features define a family of FAD-preferred reductases under physiological conditions. Our findings significantly broaden the understanding of the sequence-structure-function relationships in FPMO reductase components, uncover a structurally unique family of FAD-preferred reductases, and provide mechanistic insights into their coordination with monooxygenase partners.


  • Organizational Affiliation
    • State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FMN dependent NADH:quinone oxidoreductase
A, B
227Streptomyces albusMutation(s): 0 
Gene Names: stnCazoR
EC: 1.6.5 (PDB Primary Data), 1.7.1.17 (PDB Primary Data)
UniProt
Find proteins for L7PH54 (Streptomyces albus)
Explore L7PH54 
Go to UniProtKB:  L7PH54
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL7PH54
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free:  0.295 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.693α = 90
b = 53.046β = 90
c = 176.838γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21632007

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release