5XS6

Crystal Structure of Transketolase in complex with TPP Pichia Stipitis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

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Ligand Structure Quality Assessment 


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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: 10.1002/anie.201709799
  • Primary Citation of Related Structures:  
    5XSM, 5XSA, 5XSB, 5XRY, 5XS6, 5XTL, 5XUF, 5XTV, 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 ...

    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

    Biotechnology Center, National Chung Hsing University, Taichung City, 402, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TransketolaseA697Scheffersomyces 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP (Subject of Investigation/LOI)
Query on TPP

Download Ideal Coordinates CCD File 
F [auth A]THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.062α = 90
b = 184.795β = 90
c = 99.088γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release