Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 88.06 kDa 
• Atom Count: 6495 
• Modelled Residue Count: 780 
• Deposited Residue Count: 786 
• Unique protein chains: 1

1NR5

Crystal structure of 3-dehydroquinate synthase (DHQS) in complex with ZN2+, NAD and carbaphosphonate

• PDB DOI: 10.2210/pdb1NR5/pdb

• Classification: LYASE
• Organism(s): Aspergillus nidulans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-01-23 Released: 2003-03-18 
• Deposition Author(s): Nichols, C.E., Ren, J., Lamb, H.K., Hawkins, A.R., Stammers, D.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.232 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 

Literature

Ligand-induced Conformational Changes and a Mechanism for Domain Closure in Aspergillus nidulans Dehydroquinate Synthase

Nichols, C.E., Ren, J., Lamb, H.K., Hawkins, A.R., Stammers, D.K.

(2003) J Mol Biol 327: 129-144

• PubMed: 12614613 
• DOI: 10.1016/s0022-2836(03)00086-x
• Primary Citation of Related Structures:  
  1NR5, 1NRX, 1NUA, 1NVA, 1NVB, 1NVD, 1NVE, 1NVF


• PubMed Abstract: 
  

In order to investigate systematically substrate and cofactor-induced conformational changes in the enzyme dehydroquinate synthase (DHQS), eight structures representing a series of differently liganded states have been determined in a total of six crystal forms. DHQS in the absence of the substrate analogue carbaphosphonate, either unliganded or in the presence of NAD or ADP, is in an open form where a relative rotation of 11-13 degrees between N and C-terminal domains occurs. Analysis of torsion angle difference plots between sets of structures reveals eight rearrangements that appear relevant to domain closure and a further six related to crystal packing. Overlapping 21 different copies of the individual N and C-terminal DHQS domains further reveals a series of pivot points about which these movements occur and illustrates the way in which widely separated secondary structure elements are mechanically inter-linked to form "composite elements", which propagate structural changes across large distances. This analysis has provided insight into the basis of DHQS ligand-initiated domain closure and gives rise to the proposal of an ordered sequence of events involving substrate binding, and local rearrangements within the active site that are propagated to the hinge regions, leading to closure of the active-site cleft.

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Related Citations: 

• Identification of many crystal forms of Aspergillus nidulans dehydroquinate synthase
  Nichols, C.E., Ren, J., Lamb, H., Haldane, F., Hawkins, A.R., Stammers, D.K.
  (2001) Acta Crystallogr D Biol Crystallogr 57: 306

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Organizational Affiliation: 

Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE SYNTHASE	A, B	393	Aspergillus nidulans	Mutation(s): 0  Gene Names: aromA EC: 4.2.3.4 (PDB Primary Data), 2.5.1.19 (UniProt), 2.7.1.71 (UniProt), 4.2.1.10 (UniProt), 1.1.1.25 (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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], J [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
CRB	F [auth A], K [auth B]	[1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID C8 H15 O8 P BKLICLLAHMTUPK-UNGCPHIMSA-N
ZN	C [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO	H [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
CL	D [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.232 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.99	α = 90
b = 86.56	β = 90
c = 74.82	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-23 
• Released Date: 2003-03-18 
Deposition Author(s): Nichols, C.E., Ren, J., Lamb, H.K., Hawkins, A.R., Stammers, D.K.

Revision History  

• Version 1.0: 2003-03-18
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance