1GU1

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

• PDB DOI: https://doi.org/10.2210/pdb1GU1/pdb

• Classification: LYASE
• Organism(s): Streptomyces coelicolor
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-01-22 Released: 2002-04-12 
• Deposition Author(s): Roszak, A.W., Robinson, D.A., Krell, T., Hunter, I.S., Coggins, J.R., Lapthorn, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.200 
• R-Value Work: 0.155 

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

• PubMed: 11937054 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content

• Total Structure Weight: 204.32 kDa 
• Atom Count: 16,578 
• Modelled Residue Count: 1,788 
• Deposited Residue Count: 1,872 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A, B, C, D, E, F, G, H, I, J, K, L	156	Streptomyces coelicolor	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FA1	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
TLA	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
TRS	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
GOL	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

Binding Affinity Annotations
ID	Source	Binding 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

• 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 = 113.6	α = 90
b = 138.4	β = 90
c = 141.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-04-12 
Deposition Author(s): Roszak, A.W., Robinson, D.A., Krell, T., Hunter, I.S., Coggins, J.R., Lapthorn, A.J.

Revision History  

• 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