4D5E

Crystal Structure of recombinant wildtype CDH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Extended Reaction Scope of Thiamine Diphosphate Dependent Cyclohexane-1,2-Dione Hydrolase: From C-C Bond Cleavage to C-C Bond Ligation.

Loschonsky, S.Wacker, T.Waltzer, S.Giovannini, P.P.Mcleish, M.J.Andrade, S.L.A.Muller, M.

(2014) Angew Chem Int Ed Engl 53: 14402

  • DOI: https://doi.org/10.1002/anie.201408287
  • Primary Citation of Related Structures:  
    4D5E, 4D5G

  • PubMed Abstract: 

    ThDP-dependent cyclohexane-1,2-dione hydrolase (CDH) catalyzes the CC bond cleavage of cyclohexane-1,2-dione to 6-oxohexanoate, and the asymmetric benzoin condensation between benzaldehyde and pyruvate. One of the two reactivities of CDH was selectively knocked down by mutation experiments. CDH-H28A is much less able to catalyze the CC bond formation, while the ability for CC bond cleavage is still intact. The double variant CDH-H28A/N484A shows the opposite behavior and catalyzes the addition of pyruvate to cyclohexane-1,2-dione, resulting in the formation of a tertiary alcohol. Several acyloins of tertiary alcohols are formed with 54-94 % enantiomeric excess. In addition to pyruvate, methyl pyruvate and butane-2,3-dione are alternative donor substrates for CC bond formation. Thus, the very rare aldehyde-ketone cross-benzoin reaction has been solved by design of an enzyme variant.


  • Organizational Affiliation

    Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104 Freiburg (Germany).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYCLOHEXANE-1,2-DIONE HYDROLASE
A, B
589Azoarcus oleariusMutation(s): 0 
EC: 3.7.1.11
UniProt
Find proteins for P0CH62 (Azoarcus sp)
Explore P0CH62 
Go to UniProtKB:  P0CH62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CH62
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
P [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
TPP
Query on TPP

Download Ideal Coordinates CCD File 
D [auth A],
Q [auth B]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
2PE
Query on 2PE

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M [auth A],
V [auth B],
X [auth B]
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
P6G
Query on P6G

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H [auth A],
J [auth A]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
1PG
Query on 1PG

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I [auth A]2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
C11 H24 O6
SLNYBUIEAMRFSZ-UHFFFAOYSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
E [auth A],
R [auth B]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PG4
Query on PG4

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AA [auth B]
BA [auth B]
CA [auth B]
K [auth A]
N [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
K [auth A],
N [auth A],
O [auth A],
W [auth B],
Y [auth B],
Z [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

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L [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL
Query on CL

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F [auth A],
S [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
T [auth B],
U [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.188α = 90
b = 123.188β = 90
c = 143.07γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-05-06
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Advisory, Data collection
  • Version 1.3: 2024-05-08
    Changes: Advisory, Data collection, Database references, Derived calculations, Other