4WKO

Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with hydroxybutylthio-DADMe-Immucillin-A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

New Antibiotic Candidates against Helicobacter pylori.

Wang, S.Cameron, S.A.Clinch, K.Evans, G.B.Wu, Z.Schramm, V.L.Tyler, P.C.

(2015) J.Am.Chem.Soc. 137: 14275-14280

  • DOI: 10.1021/jacs.5b06110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Helicobacter pylori is a Gram-negative bacterium that colonizes the gut of over 50% of the world's population. It is responsible for most peptic ulcers and is an important risk factor for gastric cancer. Antibiotic treatment for H. pylori infections ...

    Helicobacter pylori is a Gram-negative bacterium that colonizes the gut of over 50% of the world's population. It is responsible for most peptic ulcers and is an important risk factor for gastric cancer. Antibiotic treatment for H. pylori infections is challenging as drug resistance has developed to antibiotics with traditional mechanisms of action. H. pylori uses an unusual pathway for menaquinone biosynthesis with 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) catalyzing an essential step. We validated MTAN as a target with a transition-state analogue of the enzyme [Wang, S.; Haapalainen, A. M.; Yan, F.; et al. Biochemistry 2012, 51, 6892-6894]. MTAN inhibitors will only be useful drug candidates if they can both include tight binding to the MTAN target and have the ability to penetrate the complex cell membrane found in Gram-negative H. pylori. Here we explore structural scaffolds for MTAN inhibition and for growth inhibition of cultured H. pylori. Sixteen analogues reported here are transition-state analogues of H. pylori MTAN with dissociation constants of 50 pM or below. Ten of these prevent growth of the H. pylori with IC90 values below 0.01 μg/mL. These remarkable compounds meet the criteria for potent inhibition and cell penetration. As a consequence, 10 new H. pylori antibiotic candidates are identified, all of which prevent H. pylori growth at concentrations 16-2000-fold lower than the five antibiotics, amoxicillin, metronidazole, levofloxacin, tetracyclin, and clarithromycin, commonly used to treat H. pylori infections. X-ray crystal structures of MTAN cocrystallized with several inhibitors show them to bind in the active site making interactions consistent with transition-state analogues.


    Related Citations: 
    • A picomolar transition state analogue inhibitor of MTAN as a specific antibiotic for Helicobacter pylori.
      Wang, S.,Haapalainen, A.M.,Yan, F.,Du, Q.,Tyler, P.C.,Evans, G.B.,Rinaldo-Matthis, A.,Brown, R.L.,Norris, G.E.,Almo, S.C.,Schramm, V.L.
      (2012) Biochemistry --: 6892


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine , New York, New York, 10461, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aminodeoxyfutalosine nucleosidase
A
245Helicobacter pylori (strain J99 / ATCC 700824)Mutation(s): 0 
Gene Names: mtnN (mtn)
EC: 3.2.2.30
Find proteins for Q9ZMY2 (Helicobacter pylori (strain J99 / ATCC 700824))
Go to UniProtKB:  Q9ZMY2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GMD
Query on GMD

Download SDF File 
Download CCD File 
A
(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-hydroxybutyl)sulfanyl]methyl}pyrrolidin-3-ol
hydroxybutylthio-DADMe-Immucillin-A
C16 H25 N5 O2 S
LDGNPMXZDVLXIT-OLZOCXBDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.158 
  • Space Group: I 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 157.256α = 90.00
b = 157.256β = 90.00
c = 157.256γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM041916

Revision History 

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2015-12-02
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations
  • Version 2.0: 2018-06-06
    Type: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary