6QYQ

Crystal structure of human thymidylate synthase (hTS) variant R175C

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report



Literature

Structural and Functional Characterization of the Human Thymidylate Synthase (hTS) Interface Variant R175C, New Perspectives for the Development of hTS Inhibitors.

Pozzi, C., Ferrari, S., Luciani, R., Costi, M.P., Mangani, S.

(2019) Molecules 24

  • DOI: 10.3390/molecules24071362
  • Primary Citation of Related Structures:  
    6QYQ

  • PubMed Abstract: 

    • Human thymidylate synthase (hTS) is pivotal for cell survival and proliferation, indeed it provides the only synthetic source of dTMP, required for DNA biosynthesis. hTS represents a validated target for anticancer chemotherapy. However, active site-targ ...

    Human thymidylate synthase (hTS) is pivotal for cell survival and proliferation, indeed it provides the only synthetic source of dTMP, required for DNA biosynthesis. hTS represents a validated target for anticancer chemotherapy. However, active site-targeting drugs towards hTS have limitations connected to the onset of resistance. Thus, new strategies have to be applied to effectively target hTS without inducing resistance in cancer cells. Here, we report the generation and the functional and structural characterization of a new hTS interface variant in which Arg175 is replaced by a cysteine. Arg175 is located at the interface of the hTS obligate homodimer and protrudes inside the active site of the partner subunit, in which it provides a fundamental contribution for substrate binding. Indeed, the R175C variant results catalytically inactive. The introduction of a cysteine at the dimer interface is functional for development of new hTS inhibitors through innovative strategies, such as the tethering approach. Structural analysis, performed through X-ray crystallography, has revealed that a cofactor derivative is entrapped inside the catalytic cavity of the hTS R175C variant. The peculiar binding mode of the cofactor analogue suggests new clues exploitable for the design of new hTS inhibitors.

    Organizational Affiliation: 

    Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy. stefano.mangani@unisi.it.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thymidylate synthase A325Homo sapiensMutation(s): 1 
Gene Names: TYMS, TS, OK/SW-cl.29
EC: 2.1.1.45
Find proteins for P04818 (Homo sapiens)
Explore P04818 
Go to UniProtKB:  P04818
NIH Common Fund Data Resources
PHAROS:  P04818
GTEx:  ENSG00000176890
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Thymidylate synthase C325Homo sapiensMutation(s): 1 
Gene Names: TYMS, TS, OK/SW-cl.29
EC: 2.1.1.45
Find proteins for P04818 (Homo sapiens)
Explore P04818 
Go to UniProtKB:  P04818
NIH Common Fund Data Resources
PHAROS:  P04818
GTEx:  ENSG00000176890
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Thymidylate synthase B325Homo sapiensMutation(s): 1 
Gene Names: TYMS, TS, OK/SW-cl.29
EC: 2.1.1.45
Find proteins for P04818 (Homo sapiens)
Explore P04818 
Go to UniProtKB:  P04818
NIH Common Fund Data Resources
PHAROS:  P04818
GTEx:  ENSG00000176890
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Thymidylate synthase D325Homo sapiensMutation(s): 1 
Gene Names: TYMS, TS, OK/SW-cl.29
EC: 2.1.1.45
Find proteins for P04818 (Homo sapiens)
Explore P04818 
Go to UniProtKB:  P04818
NIH Common Fund Data Resources
PHAROS:  P04818
GTEx:  ENSG00000176890
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME		AL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
CSX
Query on CSX		AL-PEPTIDE LINKINGC3 H7 N O3 SCYS
SCH
Query on SCH		AL-PEPTIDE LINKINGC4 H9 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.49α = 90
b = 96.52β = 90
c = 139.08γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-03-09 
  • Released Date: 2019-04-17 
    • Deposition Author(s): Pozzi, C., Mangani, M.
Funding OrganizationLocationGrant Number
European UnionLSH-2005-2.2.0-8

Revision History 

  • Version 1.0: 2019-04-17
    Type: Initial release