1DQS | pdb_00001dqs

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 (Depositor) 
  • R-Value Work: 
    0.173 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1DQS

This is version 1.4 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: https://doi.org/10.1038/28431
  • Primary Citation Related Structures: 
    1DQS

  • 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 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.


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

Macromolecule Content 

  • Total Structure Weight: 87.97 kDa 
  • Atom Count: 6,539 
  • Modeled Residue Count: 761 
  • Deposited Residue Count: 786 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (3-DEHYDROQUINATE SYNTHASE)
A, B
393Aspergillus nidulansMutation(s): 0 
Gene Names: PART OF AROMA
EC: 4.6.1.3 (PDB Primary Data), 4.2.1.10 (UniProt), 1.1.1.25 (UniProt), 4.2.3.4 (UniProt), 2.7.1.71 (UniProt), 2.5.1.19 (UniProt)
UniProt
Find proteins for P07547 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore P07547 
Go to UniProtKB:  P07547
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07547
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
CRB

Query on CRB



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B]
[1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID
C8 H15 O8 P
BKLICLLAHMTUPK-UNGCPHIMSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.224 (Depositor) 
  • R-Value Work:  0.173 (Depositor) 
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  (Full details and data files)

  • 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
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations