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

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 

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

  • 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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
156Streptomyces coelicolorMutation(s): 0 
Find proteins for P15474 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore P15474 
Go to UniProtKB:  P15474
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15474
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FA1

Download Ideal Coordinates CCD File 
AA [auth E]
DA [auth F]
GA [auth G]
JA [auth H]
M [auth A]
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]
C7 H10 O5
Query on TLA

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CA [auth E]
FA [auth F]
IA [auth G]
LA [auth H]
O [auth A]
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]
C4 H6 O6
Query on TRS

Download Ideal Coordinates CCD File 
MA [auth H],
P [auth A],
T [auth B],
ZA [auth L]
C4 H12 N O3
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth E]
EA [auth F]
HA [auth G]
KA [auth H]
N [auth A]
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]
C3 H8 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
FA1 PDBBind:  1GU1 Ki: 3.00e+4 (nM) from 1 assay(s)
Binding MOAD:  1GU1 Ki: 3.00e+4 (nM) from 1 assay(s)
BindingDB:  1GU1 Kd: 3.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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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
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description