5XRY | pdb_00005xry

Crystal Structure of Transketolase contains cysteinesufonic acid from Pichia Stipitis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.154 (Depositor), 0.154 (DCC) 
  • R-Value Work: 
    0.137 (Depositor), 0.137 (DCC) 
  • R-Value Observed: 
    0.137 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5XRY

This is version 1.1 of the entry. See complete history

Literature

The Mesomeric Effect of Thiazolium on non-Kekule Diradicals in Pichia stipitis Transketolase.

Hsu, N.S.Wang, Y.L.Lin, K.H.Chang, C.F.Lyu, S.Y.Hsu, L.J.Liu, Y.C.Chang, C.Y.Wu, C.J.Li, T.L.

(2018) Angew Chem Int Ed Engl 57: 1802-1807

  • DOI: https://doi.org/10.1002/anie.201709799
  • Primary Citation Related Structures: 
    5XRY, 5XS6, 5XSA, 5XSB, 5XSM, 5XTL, 5XTV, 5XUF, 5XVT

  • PubMed Abstract: 

    It is theoretically plausible that thiazolium mesomerizes to congeners other than carbene in a low effective dielectric binding site; especially given the energetics and uneven electronegativity of carbene groups. However, such a phenomenon has never been reported. Nine crystal structures of transketolase obtained from Pichia stipitis (TKps) are reported with subatomic resolution, where thiazolium displays an extraordinary ring-bending effect. The bent thiazolium congeners correlate with non-Kekulé diradicals because there is no gain or loss of electrons. In conjunction with biophysical and biochemical analyses, it is concluded that ring bending is a result of tautomerization of thiazolium with its non- Kekulé diradicals, exclusively in the binding site of TKps. The chemophysical properties of these thiazolium mesomers may account for the great variety of reactivities carried out by thiamine-diphosphate-containing (ThDP) enzymes. The stability of ThDP in living systems can be regulated by the levels of substrates, and hydration and dehydration, as well as diradical-mediated oxidative degradation.


  • Organizational Affiliation
    • Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 75.35 kDa 
  • Atom Count: 5,926 
  • Modeled Residue Count: 675 
  • Deposited Residue Count: 697 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transketolase697Scheffersomyces stipitis CBS 6054Mutation(s): 0 
Gene Names: TKTTKT1PICST_67105
EC: 2.2.1.1
UniProt
Find proteins for P34736 (Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545))
Explore P34736 
Go to UniProtKB:  P34736
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34736
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.154 (Depositor), 0.154 (DCC) 
  • R-Value Work:  0.137 (Depositor), 0.137 (DCC) 
  • R-Value Observed: 0.137 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.267α = 90
b = 185.551β = 90
c = 98.878γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description