4ISW | pdb_00004isw

Crystal Structure of Phosphorylated C.elegans Thymidylate Synthase in Complex with dUMP

• PDB DOI: https://doi.org/10.2210/pdb4ISW/pdb

• Classification: TRANSFERASE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-01-17 Released: 2013-12-11 
• Deposition Author(s): Wilk, P., Dowiercial, A., Banaszak, K., Jarmula, A., Rypniewski, W., Rode, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.14 Å
• R-Value Free: 
  0.270 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.234 (Depositor) 
• R-Value Observed: 
  0.236 (Depositor) 

Literature

Crystal structure of phosphoramide-phosphorylated thymidylate synthase reveals pSer127, reflecting probably pHis to pSer phosphotransfer.

Wilk, P., Jarmua, A., Ruman, T., Banaszak, K., Rypniewski, W., Ciesla, J., Dowiercia, A., Rode, W.

(2013) Bioorg Chem 52C: 44-49

• PubMed: 24321279 
• DOI: https://doi.org/10.1016/j.bioorg.2013.11.003
• Primary Citation Related Structures: 
  4ISW


• PubMed Abstract: 
  

  Crystal structure is presented of the binary complex between potassium phosphoramidate-phosphorylated recombinant C. elegans thymidylate synthase and dUMP. On each monomer a single phosphoserine residue (Ser127) was identified, instead of expected phosphohistidine. As (31)P NMR studies of both the phosphorylated protein and of potassium phosphoramidate potential to phosphorylate different amino acids point to histidine as the only possible site of the modification, thermodynamically favored intermolecular phosphotransfer from histidine to serine is suggested.

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Organizational Affiliation: 
• Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland.
Rzeszów University of Technology, Faculty of Chemistry, Bioorganic Chemistry Laboratory, 6 Powstańców Warszawy Ave., 35-959 Rzeszów, Poland.
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland.
Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland. Electronic address: [e-mail].

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: 72.49 kDa 
• Atom Count: 4,769 
• Modeled Residue Count: 580 
• Deposited Residue Count: 630 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B	315	Caenorhabditis elegans	Mutation(s): 0  EC: 2.1.1.45
UniProt
Find proteins for Q9Y052 (Caenorhabditis elegans) Explore Q9Y052  Go to UniProtKB:  Q9Y052

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UMP	C [auth A], D [auth B]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.14 Å
• R-Value Free:  0.270 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.234 (Depositor) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.436	α = 90
b = 133.436	β = 90
c = 153.969	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-11 
Deposition Author(s): Wilk, P., Dowiercial, A., Banaszak, K., Jarmula, A., Rypniewski, W., Rode, W.

Revision History  

• Version 1.0: 2013-12-11
  Type: Initial release
  
• Version 1.1: 2014-01-15
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary