6FL5

Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.263 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

The catalytic activity of serine hydroxymethyltransferase is essential for de novo nuclear dTMP synthesis in lung cancer cells.

Giardina, G.Paone, A.Tramonti, A.Lucchi, R.Marani, M.Magnifico, M.C.Bouzidi, A.Pontecorvi, V.Guiducci, G.Zamparelli, C.Rinaldo, S.Paiardini, A.Contestabile, R.Cutruzzola, F.

(2018) FEBS J 285: 3238-3253

  • DOI: https://doi.org/10.1111/febs.14610
  • Primary Citation of Related Structures:  
    6FL5

  • PubMed Abstract: 

    Cancer cells reprogramme one-carbon metabolism (OCM) to sustain growth and proliferation. Depending on cell demands, serine hydroxymethyltransferase (SHMT) dynamically changes the fluxes of OCM by reversibly converting serine and tetrahydrofolate (THF) into 5,10-methylene-THF and glycine. SHMT is a tetrameric enzyme that mainly exists in three isoforms; two localize in the cytosol (SHMT1/SHMT2α) and one (SHMT2) in the mitochondria. Both the cytosolic isoforms can also translocate to the nucleus to sustain de novo thymidylate synthesis and support cell proliferation. Finally, the expression levels of the different isoforms are regulated to a certain extent by a yet unknown crosstalk mechanism. We have designed and fully characterized a set of three SHMT1 mutants, which uncouple the oligomeric state of the enzyme from its catalytic activity. We have then investigated the effects of the mutations on SHMT1 nuclear localization, cell viability and crosstalk in lung cancer cells (A549; H1299). Our data reveal that in these cell lines de novo thymidylate synthesis requires SHMT1 to be active, regardless of its oligomeric state. We have also confirmed that the crosstalk between the cytosolic and mitochondrial SHMT actually takes place and regulates the expression of the two isoforms. Apparently, the crosstalk mechanism is independent from the oligomeric state and the catalytic activity of SHMT1. Structural data are available in the PDB under the accession number 6FL5.


  • Organizational Affiliation

    Department of Biochemical Sciences, Sapienza University of Rome, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine hydroxymethyltransferase, cytosolicA,
B [auth D],
C [auth G],
D [auth J]
471Homo sapiensMutation(s): 3 
Gene Names: SHMT1
EC: 2.1.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P34896 (Homo sapiens)
Explore P34896 
Go to UniProtKB:  P34896
PHAROS:  P34896
GTEx:  ENSG00000176974 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34896
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth D],
I [auth G],
K [auth J]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
J [auth G],
L [auth J]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.263 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.719α = 90
b = 139.719β = 90
c = 267.377γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Associazione Italiana Ricerca sul CancroItalyAIRC-IG2015 n. 16720 to FC
Regione LazioItalyFILAS-RU- 2014-1020
Fondazione Italiana Ricerca sul CancroItalyTriennal FIRC Fellowship Rif. 14843
Sapienza - University of RomeItalyC26A149EC4

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description