1DQS

CRYSTAL STRUCTURE OF DEHYDROQUINATE SYNTHASE (DHQS) COMPLEXED WITH CARBAPHOSPHONATE, NAD+ AND ZN2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of dehydroquinate synthase reveals an active site capable of multistep catalysis.

Carpenter, E.P.Hawkins, A.R.Frost, J.W.Brown, K.A.

(1998) Nature 394: 299-302

  • DOI: 10.1038/28431
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Dehydroquinate synthase (DHQS) has long been regarded as a catalytic marvel because of its ability to perform several consecutive chemical reactions in one active site. There has been considerable debate as to whether DHQS is actively involved in all ...

    Dehydroquinate synthase (DHQS) has long been regarded as a catalytic marvel because of its ability to perform several consecutive chemical reactions in one active site. There has been considerable debate as to whether DHQS is actively involved in all these steps, or whether several steps occur spontaneously, making DHQS a spectator in its own mechanism. DHQS performs the second step in the shikimate pathway, which is required for the synthesis of aromatic compounds in bacteria, microbial eukaryotes and plants. This enzyme is a potential target for new antifungal and antibacterial drugs as the shikimate pathway is absent from mammals and DHQS is required for pathogen virulence. Here we report the crystal structure of DHQS, which has several unexpected features, including a previously unobserved mode for NAD+-binding and an active-site organization that is surprisingly similar to that of alcohol dehydrogenase, in a new protein fold. The structure reveals interactions between the active site and a substrate-analogue inhibitor, which indicate how DHQS can perform multistep catalysis without the formation of unwanted by-products.


    Related Citations: 
    • Reactivation of 3-Dehydroquinate Synthase by Lanthanide Cations
      Moore, J.D., Skinner, M.A., Swatman, D.R., Hawkins, A.R., Brown, K.A.
      (1998) J Am Chem Soc 120: 7105
    • Cyclohexenyl and Cyclohexylidene Inhibitors of 3-Dehydroquinate Synthase: Active Site Interactions Relevant to Enzyme Mechanism and Inhibitor Design
      Montchamp, J.L., Frost, J.W.
      (1997) J Am Chem Soc 119: 7645
    • Efficient Independent Activity of a Monomeric, Monofunctional Dehydroquinate Synthase Derived from the N-Terminus of the Pentafunctional Arom Protein of Aspergillus Nidulans
      Moore, J.D., Coggins, J.R., Virden, R., Hawkins, A.R.
      (1994) Biochem J 301: 297
    • The Pre-Chorismate (Shikimate) and Quinate Pathways in Filamentous Fungi: Theoretical and Practical Aspects
      Hawkins, A.R., Lamb, H.K., Moore, J.D., Charles, I.G., Roberts, C.F.
      (1993) J Gen Microbiol 139: 2891
    • Overproduction in Escherichia Coli of the Dehydroquinate Synthase Domain of the Aspergillus Nidulans Pentafunctional Arom Protein
      Van Den Hombergh, J.P., Moore, J.D., Charles, I.G., Hawkins, A.R.
      (1992) Biochem J 284: 861
    • Dehydroquinate Synthase: The Use of Substrate Analogues to Probe the Early Steps of the Catalyzed Reaction
      Bender, S.L., Widlanski, T., Knowles, J.R.
      (1989) Biochemistry 28: 7560
    • The Enzymatic Conversion of 3-Deoxy-D-Arabino-Heptulosinic Acid 7-Phosphate to 5-Dehydroquinate
      Srinivasen, P.R., Rothchild, J., Sprinson, D.B.
      (1963) J Biol Chem 238: 3176

    Organizational Affiliation

    Division for Protein Structure, National Institute for Medical Research, Mill Hill, London, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (3-DEHYDROQUINATE SYNTHASE)
A, B
393Aspergillus nidulansMutation(s): 0 
Gene Names: PART OF AROMA
EC: 4.6.1.3 (PDB Primary Data), 4.2.3.4 (UniProt), 2.5.1.19 (UniProt), 2.7.1.71 (UniProt), 4.2.1.10 (UniProt), 1.1.1.25 (UniProt)
Find proteins for P07547 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Go to UniProtKB:  P07547
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
CRB
Query on CRB

Download CCD File 
A, B
[1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID
C8 H15 O8 P
BKLICLLAHMTUPK-UNGCPHIMSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.677α = 90
b = 80.81β = 90
c = 143.513γ = 90
Software Package:
Software NamePurpose
HASSPmodel building
MLPHAREphasing
DMMultimodel building
ENVATmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
HASSPphasing
DMMultiphasing
ENVATphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-07-26
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description