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: 1.80 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

  • DOI: 10.1016/s0969-2126(02)00747-5
  • Primary Citation of Related Structures:  
    1D0I, 1GU1, 1GU0, 1GTZ

  • 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 acid ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-DEHYDROQUINATE DEHYDRATASE
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
156Streptomyces coelicolorMutation(s): 0 
EC: 4.2.1.10
UniProt
Find proteins for P15474 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore P15474 
Go to UniProtKB:  P15474
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FA1
Query on FA1

Download Ideal Coordinates CCD File 
AA [auth E] , DA [auth F] , GA [auth G] , JA [auth H] , M [auth A] , NA [auth I] , Q [auth B] , QA [auth J] , 
AA [auth E],  DA [auth F],  GA [auth G],  JA [auth H],  M [auth A],  NA [auth I],  Q [auth B],  QA [auth J],  TA [auth K],  U [auth C],  WA [auth L],  X [auth D]
2,3 -ANHYDRO-QUINIC ACID
C7 H10 O5
VTEDVYGIJPLVFF-XAHCXIQSSA-N
 Ligand Interaction
TLA
Query on TLA

Download Ideal Coordinates CCD File 
CA [auth E] , FA [auth F] , IA [auth G] , LA [auth H] , O [auth A] , PA [auth I] , S [auth B] , SA [auth J] , 
CA [auth E],  FA [auth F],  IA [auth G],  LA [auth H],  O [auth A],  PA [auth I],  S [auth B],  SA [auth J],  VA [auth K],  W [auth C],  YA [auth L],  Z [auth D]
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
MA [auth H], P [auth A], T [auth B], ZA [auth L]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth E] , EA [auth F] , HA [auth G] , KA [auth H] , N [auth A] , OA [auth I] , R [auth B] , RA [auth J] , 
BA [auth E],  EA [auth F],  HA [auth G],  KA [auth H],  N [auth A],  OA [auth I],  R [auth B],  RA [auth J],  UA [auth K],  V [auth C],  XA [auth L],  Y [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FA1Ki :  30000   nM  PDBBind
FA1Kd:  30000   nM  BindingDB
FA1Ki:  30000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.6α = 90
b = 138.4β = 90
c = 141.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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