4KXW

Human transketolase in covalent complex with donor ketose D-xylulose-5-phosphate, crystal 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.095 
  • R-Value Observed: 0.095 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Sub-angstrom-resolution crystallography reveals physical distortions that enhance reactivity of a covalent enzymatic intermediate.

Ludtke, S.Neumann, P.Erixon, K.M.Leeper, F.Kluger, R.Ficner, R.Tittmann, K.

(2013) Nat Chem 5: 762-767

  • DOI: https://doi.org/10.1038/nchem.1728
  • Primary Citation of Related Structures:  
    4KXU, 4KXV, 4KXW, 4KXX, 4KXY

  • PubMed Abstract: 

    It is recognized widely that enzymes promote reactions by providing a pathway that proceeds through a transition state of lower energy. In principle, further rate enhancements could be achieved if intermediates are prevented from relaxing to their lowest energy state, and thereby reduce the barrier to the subsequent transition state. Here, we report sub-ångström-resolution crystal structures of genuine covalent reaction intermediates of transketolase. These structures reveal a pronounced out-of-plane distortion of over 20° for the covalent bond that links cofactor and substrate, and a specific elongation of the scissile substrate carbon-carbon bond (d > 1.6 Å). To achieve these distortions, the protein's conformation appears to prevent relaxation of a substrate-cofactor intermediate. The results implicate a reduced barrier to the subsequent step that is consistent with an intermediate of raised energy and leads to a more efficient overall process.


  • Organizational Affiliation

    Albrecht-von-Haller Institute, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, 37077 Göttingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transketolase637Homo sapiensMutation(s): 0 
Gene Names: TKT
EC: 2.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29401 (Homo sapiens)
Explore P29401 
Go to UniProtKB:  P29401
PHAROS:  P29401
GTEx:  ENSG00000163931 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29401
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download Ideal Coordinates CCD File 
P [auth A]THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
DX5
Query on DX5

Download Ideal Coordinates CCD File 
Q [auth A],
R [auth A]
D-XYLITOL-5-PHOSPHATE
C5 H13 O8 P
VJDOAZKNBQCAGE-VPENINKCSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
O [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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N [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.095 
  • R-Value Observed: 0.095 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.756α = 90
b = 86.017β = 125.46
c = 72.994γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
SHELXrefinement
PDB_EXTRACTdata extraction
DNAdata collection
XDSdata reduction
PHENIXphasing
SHELXLrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2019-09-04
    Changes: Data collection, Derived calculations
  • Version 2.0: 2021-08-04
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description