5XVT

Crystal Structure of Transketolase in complex with hydroxylated TPP from Pichia Stipitis, crystal 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.133 

wwPDB Validation 3D Report Full Report



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 ...

    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
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
8FL
Query on 8FL

Download CCD File 
A
2-[(2R)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-oxidanyl-2H-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate
C12 H20 N4 O8 P2 S
GFCMTWPFATXWRY-GFCCVEGCSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.133 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.22α = 90
b = 185.34β = 90
c = 99.17γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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