1AZY

STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUCES AN ACTIVE CONFORMATION OF THYMIDINE PHOSPHORYLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase.

Pugmire, M.J.Cook, W.J.Jasanoff, A.Walter, M.R.Ealick, S.E.

(1998) J.Mol.Biol. 281: 285-299

  • DOI: 10.1006/jmbi.1998.1941
  • Primary Citation of Related Structures:  1OTP, 2TPT

  • PubMed Abstract: 
  • Two new crystal forms of Escherichia coli thymidine phosphorylase (EC 2.4.2.4) have been found; a monoclinic form (space group P21) and an orthorhombic form (space group I222). These structures have been solved and compared to the previously determin ...

    Two new crystal forms of Escherichia coli thymidine phosphorylase (EC 2.4.2.4) have been found; a monoclinic form (space group P21) and an orthorhombic form (space group I222). These structures have been solved and compared to the previously determined tetragonal form (space group P43212). This comparison provides evidence of domain movement of the alpha (residues 1 to 65, 163 to 193) and alpha/beta (residues 80 to 154, 197 to 440) domains, which is thought to be critical for enzymatic activity by closing the active site cleft. Three hinge regions apparently allow the alpha and alpha/beta-domains to move relative to each other. The monoclinic model is the most open of the three models while the tetragonal model is the most closed. Phosphate binding induces formation of a hydrogen bond between His119 and Gly208, which helps to order the 115 to 120 loop that is disordered prior to phosphate binding. The formation of this hydrogen bond also appears to play a key role in the domain movement. The alpha-domain moves as a rigid body, while the alpha/beta-domain has some non-rigid body movement that is associated with the formation of the His119-Gly208 hydrogen bond. The 8 A distance between the two substrates reported for the tetragonal form indicates that it is probably not in an active conformation. However, the structural data for these two new crystal forms suggest that closing the interdomain cleft around the substrates may generate a functional active site. Molecular modeling and dynamics simulation techniques have been used to generate a hypothetical closed conformation of the enzyme. Analysis of this model suggests several residues of possible catalytic importance. The model explains observed kinetic results and satisfies requirements for efficient enzyme catalysis, most notably through the exclusion of water from the enzyme's active site.


    Related Citations: 
    • 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.Biol.Chem. 265: 14016


    Organizational Affiliation

    Department of Chemistry, Cornell University, Ithaca, NY 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDINE PHOSPHORYLASE
A, B
440Escherichia coli (strain K12)Gene Names: deoA (tpp, ttg)
EC: 2.4.2.4
Find proteins for P07650 (Escherichia coli (strain K12))
Go to UniProtKB:  P07650
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.000α = 90.00
b = 78.000β = 91.50
c = 116.500γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
XENGENdata reduction
X-PLORphasing
XENGENdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance