6JLS

Crystal Structure of FMN-dependent Cysteine Decarboxylases TvaF from Thioviridamide Biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Characterization of the FMN-Dependent Cysteine Decarboxylase from Thioviridamide Biosynthesis.

Lu, J.Li, J.Wu, Y.Fang, X.Zhu, J.Wang, H.

(2019) Org Lett 21: 4676-4679

  • DOI: https://doi.org/10.1021/acs.orglett.9b01531
  • Primary Citation of Related Structures:  
    6JLS

  • PubMed Abstract: 
  • The biosynthesis of thioviridamide-like compounds has not been elucidated. Herein, we report that TvaF from the thioviridamide biosynthetic gene cluster is an FMN-dependent cysteine decarboxylase that transforms the C-terminal cysteine of precursor peptides into a thioenol motif and exhibits high substrate flexibility ...

    The biosynthesis of thioviridamide-like compounds has not been elucidated. Herein, we report that TvaF from the thioviridamide biosynthetic gene cluster is an FMN-dependent cysteine decarboxylase that transforms the C-terminal cysteine of precursor peptides into a thioenol motif and exhibits high substrate flexibility. We resolved the crystal structure of TvaF bound with FMN at 2.24 Å resolution. Key residues for FMN binding and catalytic activity of TvaF have been identified and evaluated by mutagenesis studies.


    Organizational Affiliation

    State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative flavoprotein decarboxylase200Streptomyces olivoviridisMutation(s): 0 
Gene Names: tvaF
UniProt
Find proteins for T2HUM4 (Streptomyces olivoviridis)
Explore T2HUM4 
Go to UniProtKB:  T2HUM4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT2HUM4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: F 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 216.915α = 90
b = 216.915β = 90
c = 216.915γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references