5XTX

Crystal Structure of Transketolase in complex with TPP intermediate VII from Pichia Stipitis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Evidence of Diradicals Involved in the Yeast Transketolase Catalyzed Keto-Transferring Reactions.

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

(2018) Chembiochem 19: 2395-2402

  • DOI: https://doi.org/10.1002/cbic.201800378
  • Primary Citation of Related Structures:  
    5XPS, 5XQA, 5XQK, 5XRV, 5XT0, 5XT4, 5XTX, 5XU2, 5XU9

  • PubMed Abstract: 

    Transketolase (TK) catalyzes a reversible transfer of a two-carbon (C 2 ) unit between phosphoketose donors and phosphoaldose acceptors, for which the group-transfer reaction that follows a one- or two-electron mechanism and the force that breaks the C2"-C3" bond of the ketose donors remain unresolved. Herein, we report ultrahigh-resolution crystal structures of a TK (TKps) from Pichia stipitis in previously undiscovered intermediate states and support a diradical mechanism for a reversible group-transfer reaction. In conjunction with MS, NMR spectroscopy, EPR and computational analyses, it is concluded that the enzyme-catalyzed non-Kekulé diradical cofactor brings about the C2"-C3" bond cleavage/formation for the C 2 -unit transfer reaction, for which suppression of activation energy and activation and destabilization of enzymatic intermediates are facilitated.


  • Organizational Affiliation

    Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8ML (Subject of Investigation/LOI)
Query on 8ML

Download Ideal Coordinates CCD File 
F [auth A]2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methylidene-2-[(2S,3S,4R,5R)-1,2,3,4,5-pentakis(oxidanyl)-6-phosphonooxy-hexan-2-yl]-1,3-thiazolidin-5-yl]ethyl phosphono hydrogen phosphate
C18 H33 N4 O16 P3 S
MJHVDDPQXKRRMA-OYVLIZFGSA-N
PEG (Subject of Investigation/LOI)
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
CA (Subject of Investigation/LOI)
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.201α = 90
b = 185.345β = 90
c = 98.957γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description