2WK6

Structural features of native human thymidine phosphorylase and in complex with 5-iodouracil

• PDB DOI: https://doi.org/10.2210/pdb2WK6/pdb

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


• Deposited: 2009-06-05 Released: 2009-07-07 
• Deposition Author(s): Mitsiki, E., Papageorgiou, A.C., Iyer, S., Thiyagarajan, N., Prior, S.H., Sleep, D., Finnis, C., Acharya, K.R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.283 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 

Starting Model: experimental

Literature

Structures of Native Human Thymidine Phosphorylase and in Complex with 5-Iodouracil.

Mitsiki, E., Papageorgiou, A.C., Iyer, S., Thiyagarajan, N., Prior, S.H., Sleep, D., Finnis, C., Acharya, K.R.

(2009) Biochem Biophys Res Commun 386: 666

• PubMed: 19555658 
• DOI: https://doi.org/10.1016/j.bbrc.2009.06.104
• Primary Citation of Related Structures:  
  2WK5, 2WK6


• PubMed Abstract: 
  

  Thymidine phosphorylase (TP) first identified as platelet derived endothelial cell growth factor (PD-ECGF) plays a key role in nucleoside metabolism. Human TP (hTP) is implicated in angiogenesis and is overexpressed in several solid tumors. Here, we report the crystal structures of recombinant hTP and its complex with a substrate 5-iodouracil (5IUR) at 3.0 and 2.5A, respectively. In addition, we provide information on the role of specific residues in the enzymatic activity of hTP through mutagenesis and kinetic studies.

---

Organizational Affiliation: 

Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK.

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 PQS (software)

Macromolecule Content

• Total Structure Weight: 100.48 kDa 
• Atom Count: 6,576 
• Modelled Residue Count: 894 
• Deposited Residue Count: 964 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDINE PHOSPHORYLASE	A, B	482	Homo sapiens	Mutation(s): 0  EC: 2.4.2.4
UniProt & NIH Common Fund Data Resources
Find proteins for P19971 (Homo sapiens) Explore P19971  Go to UniProtKB:  P19971
PHAROS:  P19971 GTEx:  ENSG00000025708

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IUR	C [auth A], D [auth B]	5-IODOURACIL C4 H3 I N2 O2 KSNXJLQDQOIRIP-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IUR	PDBBind:  2WK6	Ki: 4.80e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.283 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.911	α = 90
b = 67.266	β = 90
c = 212.274	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-07 
Deposition Author(s): Mitsiki, E., Papageorgiou, A.C., Iyer, S., Thiyagarajan, N., Prior, S.H., Sleep, D., Finnis, C., Acharya, K.R.

Revision History  

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-17
  Changes: Data collection
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description