1H05 | pdb_00001h05

3-DEHYDROQUINATE DEHYDRATASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH SULPHATE

• PDB DOI: https://doi.org/10.2210/pdb1H05/pdb

• Classification: DEHYDRATASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-06-11 Released: 2002-10-24 
• Deposition Author(s): Roszak, A.W., Coggins, J.R., Lapthorn, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.191 (Depositor) 
• R-Value Work: 
  0.139 (Depositor), 0.149 (DCC) 

Starting Model: experimental

Literature

Specificity of Substrate Recognition by Type II Dehydroquinases as Revealed by Binding of Polyanions(1)

Evans, L., Roszak, A.W., Noble, L., Robinson, D., Chalk, P., Matthews, J., Coggins, J.R., Price, N., Lapthorn, A.J.

(2002) FEBS Lett 530: 24

• PubMed: 12387860 
• DOI: https://doi.org/10.1016/s0014-5793(02)03346-x
• Primary Citation Related Structures: 
  1H05


• PubMed Abstract: 
  

  The interactions between the polyanionic ligands phosphate and sulphate and the type II dehydroquinases from Streptomyces coelicolor and Mycobacterium tuberculosis have been characterised using a combination of structural and kinetic methods. From both approaches, it is clear that interactions are more complex in the case of the latter enzyme. The data provide new insights into the differences between the two enzymes in terms of substrate recognition and catalytic efficiency and may also explain the relative potencies of rationally designed inhibitors. An improved route to the synthesis of the substrate 3-dehydroquinic acid (dehydroquinate) is described.

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Organizational Affiliation: 
• Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, UK.

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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 16.06 kDa 
• Atom Count: 1,293 
• Modeled Residue Count: 138 
• Deposited Residue Count: 146 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A	146	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  EC: 4.2.1.10
UniProt
Find proteins for P9WPX7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPX7  Go to UniProtKB:  P9WPX7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.191 (Depositor) 
• R-Value Work:  0.139 (Depositor), 0.149 (DCC) 

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.635	α = 90
b = 126.635	β = 90
c = 126.635	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: 2002-10-24 
Deposition Author(s): Roszak, A.W., Coggins, J.R., Lapthorn, A.J.

Revision History  

• Version 1.0: 2002-10-24
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description