4GYH | pdb_00004gyh

Structure of human thymidylate synthase at high salt conditions

• PDB DOI: https://doi.org/10.2210/pdb4GYH/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-09-05 Released: 2012-10-03 
• Deposition Author(s): Brunn, N., Dibrov, S., Hermann, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.280 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Analysis of mRNA recognition by human thymidylate synthase.

Brunn, N.D., Dibrov, S.M., Kao, M.B., Ghassemian, M., Hermann, T.

(2014) Biosci Rep 34: e00168-e00168

• PubMed: 25423174 
• DOI: https://doi.org/10.1042/BSR20140137
• Primary Citation Related Structures: 
  4GYH, 4H1I


• PubMed Abstract: 
  

  Expression of hTS (human thymidylate synthase), a key enzyme in thymidine biosynthesis, is regulated on the translational level through a feedback mechanism that is rarely found in eukaryotes. At low substrate concentrations, the ligand-free enzyme binds to its own mRNA and stabilizes a hairpin structure that sequesters the start codon. When in complex with dUMP (2'-deoxyuridine-5'-monophosphate) and a THF (tetrahydrofolate) cofactor, the enzyme adopts a conformation that is unable to bind and repress expression of mRNA. Here, we have used a combination of X-ray crystallography, RNA mutagenesis and site-specific cross-linking studies to investigate the molecular recognition of TS mRNA by the hTS enzyme. The interacting mRNA region was narrowed to the start codon and immediately flanking sequences. In the hTS enzyme, a helix-loop-helix domain on the protein surface was identified as the putative RNA-binding site.

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Organizational Affiliation: 
• *Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, U.S.A.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.65 kDa 
• Atom Count: 2,135 
• Modeled Residue Count: 263 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A	318	Homo sapiens	Mutation(s): 0  Gene Names: TYMS, TS, OK/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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.280 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.194	α = 90
b = 96.194	β = 90
c = 83.275	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Brunn, N., Dibrov, S., Hermann, T.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Database references
• Version 1.2: 2015-01-28
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description