7XZP

Formate-tetrahydrofolate ligase in complex with berberine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Identification of FtfL as a novel target of berberine in intestinal bacteria.

Yan, J.Fang, C.Yang, G.Li, J.Liu, Y.Zhang, L.Yang, P.Fang, J.Gu, Y.Zhang, Y.Jiang, W.

(2023) BMC Biol 21: 280-280

  • DOI: https://doi.org/10.1186/s12915-023-01778-w
  • Primary Citation of Related Structures:  
    7XZN, 7XZO, 7XZP

  • PubMed Abstract: 

    Berberine (BBR) is a commonly used anti-intestinal inflammation drug, and its anti-cancer activity has been found recently. BBR can intervene and control malignant colorectal cancer (CRC) through intestinal microbes, but the direct molecular target and related mechanism are unclear. This study aimed to identify the target of BBR and dissect related mechanisms against the occurrence and development of CRC from the perspective of intestinal microorganisms. Here, we found that BBR inhibits the growth of several CRC-driving bacteria, especially Peptostreptococcus anaerobius. By using a biotin-conjugated BBR derivative, we identified the protein FtfL (formate tetrahydrofolate ligase), a key enzyme in C1 metabolism, is the molecular target of BBR in P. anaerobius. BBR exhibits strong binding affinity and potent inhibition on FtfL. Based on this, we determined the crystal structure of PaFtfL (P. anaerobius FtfL)-BBR complex and found that BBR can not only interfere with the conformational flexibility of PaFtfL tetramer by wedging the tetramer interface but also compete with its substrate ATP for binding within the active center. In addition, the enzymatic activities of FtfL homologous proteins in human tumor cells can also be inhibited by BBR. In summary, our study has identified FtfL as a direct target of BBR and uncovered molecular mechanisms involved in the anti-CRC of BBR. BBR interferes with intestinal pathogenic bacteria by targeting FtfLs, suggesting a new means for controlling the occurrence and development of CRC.


  • Organizational Affiliation

    CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Formate--tetrahydrofolate ligase
A, B
562Peptostreptococcus anaerobiusMutation(s): 0 
Gene Names: fhsNCTC11460_01517
EC: 6.3.4.3
UniProt
Find proteins for A0A379CIH2 (Peptostreptococcus anaerobius)
Explore A0A379CIH2 
Go to UniProtKB:  A0A379CIH2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A379CIH2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BER (Subject of Investigation/LOI)
Query on BER

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
K [auth B],
L [auth B]
BERBERINE
C20 H18 N O4
YBHILYKTIRIUTE-UHFFFAOYSA-N
PRO
Query on PRO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
M [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.26α = 90
b = 205.21β = 90
c = 107.61γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MoRDaphasing

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)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-12-20
    Changes: Database references