2WK5 | pdb_00002wk5

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

PDB DOI: https://doi.org/10.2210/pdb2WK5/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: 2.99 Å
R-Value Free:
0.284 (Depositor)
R-Value Work:
0.207 (Depositor)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.bbrc.2009.06.104
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 200.11 kDa
Atom Count: 13,034
Modeled Residue Count: 1,787
Deposited Residue Count: 1,928
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDINE PHOSPHORYLASE	A, B, C, D	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19971
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.99 Å
R-Value Free: 0.284 (Depositor)
R-Value Work: 0.207 (Depositor)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.532	α = 90
b = 77.188	β = 98.04
c = 100.878	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-07-07

Deposition Author(s):

Revision History (Full details and data files)

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: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description