3ZOK

Structure of 3-Dehydroquinate Synthase from Actinidia chinensis in complex with NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Biochemical and structural characterisation of dehydroquinate synthase from the New Zealand kiwifruit Actinidia chinensis.

Mittelstadt, G.Negron, L.Schofield, L.R.Marsh, K.Parker, E.J.

(2013) Arch Biochem Biophys 537: 185-191

  • DOI: https://doi.org/10.1016/j.abb.2013.07.022
  • Primary Citation of Related Structures:  
    3ZOK

  • PubMed Abstract: 

    One of the novel aspects of kiwifruit is the presence of a high level of quinic acid which contributes to the flavour of the fruit. Quinic acid metabolism intersects with the shikimate pathway, which is responsible for the de novo biosynthesis of primary and secondary aromatic metabolites. The gene encoding the enzyme which catalyses the second step of the shikimate pathway, dehydroquinate synthase (DHQS), from the New Zealand kiwifruit Actinidia chinensis was identified, cloned and expressed. A. chinensis DHQS was activated by divalent metal ions, and was found to require NAD(+) for catalysis. The protein was crystallised and the structure was solved, revealing a homodimeric protein. Each monomer has a NAD(+) binding site nestled between the distinct N- and C-terminal domains. In contrast to other microbial DHQSs, which show an open conformation in the absence of active site ligands, A. chinensis DHQS adopts a closed conformation. This is the first report of the structure of a DHQS from a plant source.


  • Organizational Affiliation

    Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, PO Box 4800, Christchurch 8140, New Zealand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-DEHYDROQUINATE SYNTHASE
A, B, C, D
378Actinidia chinensisMutation(s): 0 
EC: 4.2.3.4
UniProt
Find proteins for U3KRF2 (Actinidia chinensis var. chinensis)
Explore U3KRF2 
Go to UniProtKB:  U3KRF2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU3KRF2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
DA [auth D],
H [auth A],
P [auth B],
W [auth C]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
2PE
Query on 2PE

Download Ideal Coordinates CCD File 
Q [auth B]NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
X [auth C]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
R [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
EA [auth D],
FA [auth D],
GA [auth D],
I [auth A],
J [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
E [auth A]
F [auth A]
AA [auth D],
BA [auth D],
CA [auth D],
E [auth A],
F [auth A],
G [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
T [auth C],
U [auth C],
V [auth C],
Z [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GLY
Query on GLY

Download Ideal Coordinates CCD File 
HA [auth D],
IA [auth D],
K [auth A],
S [auth B],
Y [auth C]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.06α = 90
b = 150.97β = 101.25
c = 84.75γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

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: 2013-09-25
    Changes: Database references
  • Version 1.2: 2018-11-14
    Changes: Data collection, Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description