6YAJ

Split gene transketolase, inactive beta4 tetramer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.178 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A 'Split-Gene' Transketolase From the Hyper-Thermophilic Bacterium Carboxydothermus hydrogenoformans : Structure and Biochemical Characterization.

James, P.Isupov, M.N.De Rose, S.A.Sayer, C.Cole, I.S.Littlechild, J.A.

(2020) Front Microbiol 11: 592353-592353

  • DOI: https://doi.org/10.3389/fmicb.2020.592353
  • Primary Citation of Related Structures:  
    6YAJ, 6YAK

  • PubMed Abstract: 

    A novel transketolase has been reconstituted from two separate polypeptide chains encoded by a 'split-gene' identified in the genome of the hyperthermophilic bacterium, Carboxydothermus hydrogenoformans . The reconstituted active α 2 β 2 tetrameric enzyme has been biochemically characterized and its activity has been determined using a range of aldehydes including glycolaldehyde, phenylacetaldehyde and cyclohexanecarboxaldehyde as the ketol acceptor and hydroxypyruvate as the donor. This reaction proceeds to near 100% completion due to the release of the product carbon dioxide and can be used for the synthesis of a range of sugars of interest to the pharmaceutical industry. This novel reconstituted transketolase is thermally stable with no loss of activity after incubation for 1 h at 70°C and is stable after 1 h incubation with 50% of the organic solvents methanol, ethanol, isopropanol, DMSO, acetonitrile and acetone. The X-ray structure of the holo reconstituted α 2 β 2 tetrameric transketolase has been determined to 1.4 Å resolution. In addition, the structure of an inactive tetrameric β 4 protein has been determined to 1.9 Å resolution. The structure of the active reconstituted α 2 β 2 enzyme has been compared to the structures of related enzymes; the E1 component of the pyruvate dehydrogenase complex and D-xylulose-5-phosphate synthase, in an attempt to rationalize differences in structure and substrate specificity between these enzymes. This is the first example of a reconstituted 'split-gene' transketolase to be biochemically and structurally characterized allowing its potential for industrial biocatalysis to be evaluated.


  • Organizational Affiliation

    Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-terminal chain of split transketolase from Carboxydothermus hydrogenoformansA [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth DDD]
341Carboxydothermus hydrogenoformansMutation(s): 0 
EC: 2.2.1.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
O [auth BBB]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth AAA]
J [auth BBB]
N [auth BBB]
S [auth CCC]
T [auth DDD]
G [auth AAA],
J [auth BBB],
N [auth BBB],
S [auth CCC],
T [auth DDD],
Y [auth DDD]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth AAA]
F [auth AAA]
H [auth AAA]
I [auth AAA]
K [auth BBB]
E [auth AAA],
F [auth AAA],
H [auth AAA],
I [auth AAA],
K [auth BBB],
L [auth BBB],
M [auth BBB],
P [auth CCC],
Q [auth CCC],
R [auth CCC],
U [auth DDD],
V [auth DDD],
W [auth DDD],
X [auth DDD],
Z [auth DDD]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.878α = 90
b = 101.878β = 90
c = 164.546γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/L002035/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description