Crystal structure of E. faecium SHMT in complex with (+)-SHIN-1 and PLP-Ser

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

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Serine hydroxymethyltransferase as a potential target of antibacterial agents acting synergistically with one-carbon metabolism-related inhibitors.

Makino, Y.Oe, C.Iwama, K.Suzuki, S.Nishiyama, A.Hasegawa, K.Okuda, H.Hirata, K.Ueno, M.Kawaji, K.Sasano, M.Usui, E.Hosaka, T.Yabuki, Y.Shirouzu, M.Katsumi, M.Murayama, K.Hayashi, H.Kodama, E.N.

(2022) Commun Biol 5: 619-619

  • DOI: https://doi.org/10.1038/s42003-022-03555-x
  • Primary Citation of Related Structures:  
    7V3D, 7X5N, 7X5O

  • PubMed Abstract: 

    Serine hydroxymethyltransferase (SHMT) produces 5,10-methylenetetrahydrofolate (CH 2 -THF) from tetrahydrofolate with serine to glycine conversion. SHMT is a potential drug target in parasites, viruses and cancer. (+)-SHIN-1 was developed as a human SHMT inhibitor for cancer therapy. However, the potential of SHMT as an antibacterial target is unknown. Here, we show that (+)-SHIN-1 bacteriostatically inhibits the growth of Enterococcus faecium at a 50% effective concentration of 10 -11 M and synergistically enhances the antibacterial activities of several nucleoside analogues. Our results, including crystal structure analysis, indicate that (+)-SHIN-1 binds tightly to E. faecium SHMT (efmSHMT). Two variable loops in SHMT are crucial for inhibitor binding, and serine binding to efmSHMT enhances the affinity of (+)-SHIN-1 by stabilising the loop structure of efmSHMT. The findings highlight the potency of SHMT as an antibacterial target and the possibility of developing SHMT inhibitors for treating bacterial, viral and parasitic infections and cancer.

  • Organizational Affiliation

    Department of Infectious Diseases, Tohoku University Graduate School of Medicine, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine hydroxymethyltransferase
A, B
417Enterococcus faeciumMutation(s): 0 
Gene Names: 
Find proteins for I3U4H4 (Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO))
Explore I3U4H4 
Go to UniProtKB:  I3U4H4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3U4H4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5M5 (Subject of Investigation/LOI)
Query on 5M5

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
C24 H24 N4 O2
PLS (Subject of Investigation/LOI)
Query on PLS

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
C11 H17 N2 O8 P
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.35α = 90
b = 119.35β = 90
c = 162.588γ = 90
Software Package:
Software NamePurpose
BSSdata collection
XDSdata reduction
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection