4KXV

Human transketolase in covalent complex with donor ketose D-xylulose-5-phosphate, crystal 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.114 
  • R-Value Work: 0.094 
  • R-Value Observed: 0.094 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1038/nchem.1728
  • Primary Citation of Related Structures:  
    4KXY, 4KXU, 4KXV, 4KXW, 4KXX

  • 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 lo ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TransketolaseA637Homo sapiensMutation(s): 0 
Gene Names: TKT
EC: 2.2.1.1
Find proteins for P29401 (Homo sapiens)
Explore P29401 
Go to UniProtKB:  P29401
NIH Common Fund Data Resources
PHAROS  P29401
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TDP
Query on TDP

Download CCD File 
A
THIAMIN DIPHOSPHATE
C12 H18 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-N
 Ligand Interaction
DX5
Query on DX5

Download CCD File 
A
D-XYLITOL-5-PHOSPHATE
C5 H13 O8 P
VJDOAZKNBQCAGE-VPENINKCSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
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: 0.114 
  • R-Value Work: 0.094 
  • R-Value Observed: 0.094 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.67α = 90
b = 85.98β = 125.3
c = 73γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
SHELXrefinement
PDB_EXTRACTdata extraction
DNAdata collection
XDSdata reduction
PHENIXphasing
SHELXLrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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