6R2E | pdb_00006r2e

Crystal structure of the human thymidylate synthase (hTS) interface variant Q62R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.258 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.196 (Depositor) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Evidence of Destabilization of the Human Thymidylate Synthase (hTS) Dimeric Structure Induced by the Interface Mutation Q62R.

Pozzi, C.Lopresti, L.Santucci, M.Costi, M.P.Mangani, S.

(2019) Biomolecules 9

  • DOI: https://doi.org/10.3390/biom9040134
  • Primary Citation Related Structures: 
    6R2E

  • PubMed Abstract: 

    In human cells, thymidylate synthase (TS) provides the only source of 2'-deoxythymidyne-5'-monophosphate (dTMP), which is required for DNA biosynthesis. Because of its pivotal role, human TS (hTS) represents a validated target for anticancer chemotherapy. Nonetheless, the efficacy of drugs blocking the hTS active site has limitations due to the onset of resistance in cancer cells, requiring the identification of new strategies to effectively inhibit this enzyme. Human TS works as an obligate homodimer, making the inter-subunit interface an attractive targetable area. Here, we report the design and investigation of a new hTS variant, in which Gln62, located at the dimer interface, has been replaced by arginine in order to destabilize the enzyme quaternary assembly. The hTS Q62R variant has been characterized though kinetic assay, thermal denaturation analysis and X-ray crystallography. Our results provide evidence that hTS Q62R has a reduced melting temperature. The effective destabilization of the TS quaternary structure is also confirmed by structural analysis, showing that the introduced mutation induces a slight aperture of the hTS dimer. The generation of hTS variants having a more accessible interface area can facilitate the screening of interface-targeting molecules, providing key information for the rational design of innovative hTS interface inhibitors.


  • Organizational Affiliation
    • Department of Biotechnology, Chemistry and Pharmacy-Department of Excellence 2018-2020, University of Siena, 53100 Siena, Italy. pozzi4@unisi.it.

Macromolecule Content 

  • Total Structure Weight: 304.63 kDa 
  • Atom Count: 21,357 
  • Modeled Residue Count: 2,305 
  • Deposited Residue Count: 2,600 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thymidylate synthase325Homo sapiensMutation(s): 1 
Gene Names: TYMSTSOK/SW-cl.29
EC: 2.1.1.45
UniProt & NIH Common Fund Data Resources
Find proteins for P04818 (Homo sapiens)
Explore P04818 
Go to UniProtKB:  P04818
PHAROS:  P04818
GTEx:  ENSG00000176890 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04818
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Thymidylate synthaseG [auth E],
H [auth G]
325Homo sapiensMutation(s): 1 
Gene Names: TYMSTSOK/SW-cl.29
EC: 2.1.1.45
UniProt & NIH Common Fund Data Resources
Find proteins for P04818 (Homo sapiens)
Explore P04818 
Go to UniProtKB:  P04818
PHAROS:  P04818
GTEx:  ENSG00000176890 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04818
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FFO

Query on FFO



Download:Ideal Coordinates CCD File
AA [auth B]
EA [auth F]
HA [auth H]
K [auth A]
LA [auth E]
AA [auth B],
EA [auth F],
HA [auth H],
K [auth A],
LA [auth E],
PA [auth G],
Q [auth C],
U [auth D]
N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid
C20 H23 N7 O7
VVIAGPKUTFNRDU-STQMWFEESA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
CA [auth F]
DA [auth F]
FA [auth H]
GA [auth H]
I [auth A]
CA [auth F],
DA [auth F],
FA [auth H],
GA [auth H],
I [auth A],
J [auth A],
JA [auth E],
KA [auth E],
N [auth C],
NA [auth G],
O [auth C],
OA [auth G],
P [auth C],
S [auth D],
T [auth D],
Y [auth B],
Z [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
IA [auth H],
V [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
BA [auth B]
L [auth A]
M [auth A]
MA [auth E]
QA [auth G]
BA [auth B],
L [auth A],
M [auth A],
MA [auth E],
QA [auth G],
R [auth C],
W [auth D],
X [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CME
Query on CME
A
B [auth C]
C [auth D]
D [auth B]
E [auth F]
A,
B [auth C],
C [auth D],
D [auth B],
E [auth F],
F [auth H]
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
SCH
Query on SCH
G [auth E],
H [auth G]
L-PEPTIDE LINKINGC4 H9 N O2 S2CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.258 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.196 (Depositor) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.939α = 90
b = 167.07β = 90
c = 189.97γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Association for Cancer ResearchItalyAIRC IG16977

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description