6LLA

Crystal structure of Providencia alcalifaciens 3-dehydroquinate synthase (DHQS) in complex with Mg2+ and NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and Biochemical Analyses Reveal that Chlorogenic Acid Inhibits the Shikimate Pathway.

Neetu, N.Katiki, M.Dev, A.Gaur, S.Tomar, S.Kumar, P.

(2020) J Bacteriol 202

  • DOI: 10.1128/JB.00248-20
  • Primary Citation of Related Structures:  
    6LK2, 6LLA

  • PubMed Abstract: 
  • Chlorogenic acid (CGA) is a phenolic compound with well-known antibacterial properties against pathogens. In this study, structural and biochemical characterization display the inhibitory role of CGA against the enzyme of the shikimate pathway, a wel ...

    Chlorogenic acid (CGA) is a phenolic compound with well-known antibacterial properties against pathogens. In this study, structural and biochemical characterization display the inhibitory role of CGA against the enzyme of the shikimate pathway, a well characterized drug target in several pathogens. Here, we report the crystal structures of dehydroquinate synthase (DHQS), the second enzyme of the shikimate pathway, from Providencia alcalifaciens ( Pa DHQS), in binary complex with NAD and ternary complex with NAD and CGA. Structural analyses reveal that CGA occupies the substrate position in the active site of Pa DHQS, which disables domain movements, leaving the enzyme in open and catalysis incompetent state. The binding analyses by ITC and SPR show that CGA binds to Pa DHQS with a K D value of 6.3 μM and 0.5 μM respectively. In vitro e nzyme inhibition studies show that CGA inhibits Pa DHQS with a K i of 235 ± 21 μM; while it inhibits the growth of Providencia alcalifaciens , Moraxella catarrhalis , Staphylococcus aureus and Escherichia coli with MIC values of 60 to 100 μM. In the presence of aromatic amino acids supplied externally, CGA doesn't show the toxic effect. These results, along with the observations of the inhibition of DAHP regulatory domain by CGA in our previous study, suggest that CGA binds to shikimate pathway enzymes with high affinity and inhibits their catalysis, and can be further exploited for designing novel drug-like molecules. Importance The shikimate pathway is an attractive target for the development of herbicides and antimicrobial agents as it is essential in plants, bacteria and apicomplexan parasites, but absent in humans. The enzymes of shikimate pathway are conserved among bacteria. Thus, the inhibitors of the shikimate pathway will act on wide range of pathogens. We have identified that chlorogenic acid targets the enzymes of shikimate pathway. The crystal structure of dehydroquinate synthase the second enzyme of the pathway, in complex with chlorogenic acid and enzymatic inhibition studies explain the mechanism of inhibition of chlorogenic acid. These results suggest that chlorogenic acid has a good chemical scaffold and have important implications for the further development as potent inhibitor of shikimate pathway enzymes.


    Organizational Affiliation

    From the Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India -247667 pravshai@gmail.com pravindra.kumar@bt.iitr.ac.in.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-dehydroquinate synthaseA, B, C, D375Providencia alcalifaciens F90-2004Mutation(s): 0 
Gene Names: aroBHMPREF1562_0140
EC: 4.2.3.4
Find proteins for X6Q997 (Providencia alcalifaciens F90-2004)
Explore X6Q997 
Go to UniProtKB:  X6Q997
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
A, B, C
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.39α = 90
b = 59.92β = 93.95
c = 143.8γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science and Engineering Research Board (SERB)India--

Revision History 

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Database references