1GU1

Crystal structure of type II dehydroquinase from Streptomyces coelicolor complexed with 2,3-anhydro-quinic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Structure and Mechanism of the Type II Dehydroquinase from Streptomyces Coelicolor

Roszak, A.W.Robinson, D.A.Krell, T.Hunter, I.S.Fredrickson, M.Abell, C.Coggins, J.R.Lapthorn, A.J.

(2002) Structure 10: 493

  • Primary Citation of Related Structures:  1D0I, 1GTZ, 1GU0
  • Also Cited By: 2BT4

  • PubMed Abstract: 
  • The structure of the type II DHQase from Streptomyces coelicolor has been solved and refined to high resolution in complexes with a number of ligands, including dehydroshikimate and a rationally designed transition state analogue, 2,3-anhydro-quinic ...

    The structure of the type II DHQase from Streptomyces coelicolor has been solved and refined to high resolution in complexes with a number of ligands, including dehydroshikimate and a rationally designed transition state analogue, 2,3-anhydro-quinic acid. These structures define the active site of the enzyme and the role of key amino acid residues and provide snap shots of the catalytic cycle. The resolution of the flexible lid domain (residues 21-31) shows that the invariant residues Arg23 and Tyr28 close over the active site cleft. The tyrosine acts as the base in the initial proton abstraction, and evidence is provided that the reaction proceeds via an enol intermediate. The active site of the structure of DHQase in complex with the transition state analog also includes molecules of tartrate and glycerol, which provide a basis for further inhibitor design.


    Organizational Affiliation

    Department of Chemistry, Institute of Biomedical and Life Sciences, University of Glasgow, Scotland, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-DEHYDROQUINATE DEHYDRATASE
A, B, C, D, E, F, G, H, I, J, K, L
156Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)Gene Names: aroQ
EC: 4.2.1.10
Find proteins for P15474 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Go to UniProtKB:  P15474
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
TLA
Query on TLA

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Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
FA1
Query on FA1

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
2,3 -ANHYDRO-QUINIC ACID
C7 H10 O5
VTEDVYGIJPLVFF-XAHCXIQSSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, B, H, L
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FA1Kd: 30000 nM (100) BINDINGDB
FA1Ki: 30000 nM BINDINGMOAD
FA1Ki: 30000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 113.600α = 90.00
b = 138.400β = 90.00
c = 141.500γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-04-12
    Type: Initial release
  • Version 1.1: 2011-09-28
    Type: Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2013-07-24
    Type: Data collection, Structure summary