1TPT | pdb_00001tpt

THREE-DIMENSIONAL STRUCTURE OF THYMIDINE PHOSPHORYLASE FROM ESCHERICHIA COLI AT 2.8 ANGSTROMS RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1TPT/pdb

• Classification: THYMIDINE PHOSPHORYLASE
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1990-06-14 Released: 1991-07-15 
• Deposition Author(s): Walter, M.R., Cook, W.J., Cole, L.B., Short, S.A., Koszalka, G.W., Krenitsky, T.A., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Observed: 
  0.280 (Depositor) 

Literature

Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 A resolution.

Walter, M.R., Cook, W.J., Cole, L.B., Short, S.A., Koszalka, G.W., Krenitsky, T.A., Ealick, S.E.

(1990) J Biological Chem 265: 14016-14022

• PubMed: 2199449 
• DOI: https://doi.org/10.2210/pdb1tpt/pdb
• Primary Citation Related Structures: 
  1TPT


• PubMed Abstract: 
  

  The three-dimensional structure of thymidine phosphorylase from Escherichia coli has been determined at 2.8 A resolution using multiple-isomorphous-replacement techniques. The amino acid sequence deduced from the deoA DNA sequence is also reported. Thymidine phosphorylase exists in the crystal as an S-shaped dimer in which the subunits are related by a crystallographic 2-fold axis. Each subunit is composed of a small alpha-helical domain of six helices and a large alpha/beta domain. The alpha/beta domain includes a six-stranded mixed beta-sheet and a four-stranded antiparallel beta-sheet. The active site has been identified by difference Fourier analyses of the binding of thymine and thymidine and lies in a cavity between the small and large domains. The central beta-sheet is splayed open to accommodate a putative phosphate-binding site which is probably occupied by a sulfate ion in the crystal.

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Organizational Affiliation: 
• Department of Biochemistry, University of Alabama, Birmingham 35294.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 47.46 kDa 
• Atom Count: 454 
• Modeled Residue Count: 440 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDINE PHOSPHORYLASE	A	440	Escherichia coli	Mutation(s): 0  EC: 2.4.2.4
UniProt
Find proteins for P07650 (Escherichia coli (strain K12)) Explore P07650  Go to UniProtKB:  P07650

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TDR	C [auth A]	THYMINE C5 H6 N2 O2 RWQNBRDOKXIBIV-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Observed: 0.280 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133	α = 90
b = 133	β = 90
c = 67.5	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1991-07-15 
Deposition Author(s): Walter, M.R., Cook, W.J., Cole, L.B., Short, S.A., Koszalka, G.W., Krenitsky, T.A., Ealick, S.E.

Revision History  

• Version 1.0: 1991-07-15
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Other