4YHA

Crystal structure of the complex of Helicobacter pylori alpha-Carbonic Anhydrase with methazolamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structural Basis for the Inhibition of Helicobacter pylori alpha-Carbonic Anhydrase by Sulfonamides.

Modakh, J.K.Liu, Y.C.Machuca, M.A.Supuran, C.T.Roujeinikova, A.

(2015) Plos One 10: e0127149-e0127149

  • DOI: 10.1371/journal.pone.0127149
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Periplasmic α-carbonic anhydrase of Helicobacter pylori (HpαCA), an oncogenic bacterium in the human stomach, is essential for its acclimation to low pH. It catalyses the conversion of carbon dioxide to bicarbonate using Zn(II) as the cofactor. In H. ...

    Periplasmic α-carbonic anhydrase of Helicobacter pylori (HpαCA), an oncogenic bacterium in the human stomach, is essential for its acclimation to low pH. It catalyses the conversion of carbon dioxide to bicarbonate using Zn(II) as the cofactor. In H. pylori, Neisseria spp., Brucella suis and Streptococcus pneumoniae this enzyme is the target for sulfonamide antibacterial agents. We present structural analysis correlated with inhibition data, on the complexes of HpαCA with two pharmacological inhibitors of human carbonic anhydrases, acetazolamide and methazolamide. This analysis reveals that two sulfonamide oxygen atoms of the inhibitors are positioned proximal to the putative location of the oxygens of the CO2 substrate in the Michaelis complex, whilst the zinc-coordinating sulfonamide nitrogen occupies the position of the catalytic water molecule. The structures are consistent with acetazolamide acting as site-directed, nanomolar inhibitors of the enzyme by mimicking its reaction transition state. Additionally, inhibitor binding provides insights into the channel for substrate entry and product exit. This analysis has implications for the structure-based design of inhibitors of bacterial carbonic anhydrases.


    Organizational Affiliation

    Laboratorio di Chimica Bioinorganica, Polo Scientifico, Università degli Studi di Firenze, Via della Lastruccia 3, Sesto Fiorentino (Florence) Italy; Neurofarba Department, Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Via U. Schiff 6, Sesto Fiorentino (Firenze), Italy.,Department of Microbiology, Faculty of Biomedical and Psychological Sciences, Monash University, Clayton, Victoria, Australia.,Department of Microbiology, Faculty of Biomedical and Psychological Sciences, Monash University, Clayton, Victoria, Australia; Department of Biochemistry and Molecular Biology, Faculty of Biomedical and Psychological Sciences, Monash University, Clayton, Victoria, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-carbonic anhydrase
A, B, C, D, E, F, G, H
234Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Find proteins for A0A0M3KL20 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  A0A0M3KL20
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, E, G, H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
C, D, E, G
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MZM
Query on MZM

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
N-(3-methyl-5-sulfamoyl-1,3,4-thiadiazol-2(3H)-ylidene)acetamide
Methazolamide
C5 H8 N4 O3 S2
FLOSMHQXBMRNHR-DAXSKMNVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MZMKi: 225 nM (99) BINDINGDB
MZMKi: 225 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.450α = 90.00
b = 135.650β = 90.05
c = 166.580γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
iMOSFLMdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-12-16
    Type: Structure summary
  • Version 2.0: 2017-11-22
    Type: Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary