4FFS

Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Helicobacter pylori with butyl-thio-DADMe-Immucillin-A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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 51: 6892-6894

  • DOI: 10.1021/bi3009664
  • Also Cited By: 4WKO, 4YO8, 4YNB, 4WKP, 4WKN

  • PubMed Abstract: 
  • Campylobacter and Helicobacter species express a 6-amino-6-deoxyfutalosine N-ribosylhydrolase (HpMTAN) proposed to function in menaquinone synthesis. BuT-DADMe-ImmA is a 36 pM transition state analogue of HpMTAN, and the crystal structure of the enzy ...

    Campylobacter and Helicobacter species express a 6-amino-6-deoxyfutalosine N-ribosylhydrolase (HpMTAN) proposed to function in menaquinone synthesis. BuT-DADMe-ImmA is a 36 pM transition state analogue of HpMTAN, and the crystal structure of the enzyme-inhibitor complex reveals the mechanism of inhibition. BuT-DADMe-ImmA has a MIC(90) value of <8 ng/mL for Helicobacter pylori growth but does not cause growth arrest in other common clinical pathogens, thus demonstrating potential as an H. pylori-specific antibiotic.


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MTA/SAH nucleosidase
A
239Helicobacter 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BIG
Query on BIG

Download SDF File 
Download CCD File 
A
(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(butylsulfanyl)methyl]pyrrolidin-3-ol
butylthio-DADMe-Immucillin A
C16 H25 N5 O S
LTSUEVPGSXUJHT-OLZOCXBDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BIGKd: 0.036 nM BINDINGMOAD
BIGKd: 0.036 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.161 
  • Space Group: I 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 157.732α = 90.00
b = 157.732β = 90.00
c = 157.732γ = 90.00
Software Package:
Software NamePurpose
XDisplayFdata collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-26
    Type: Initial release