5K1Z

Joint X-ray/neutron structure of MTAN complex with p-ClPh-Thio-DADMe-ImmA


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.253 

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Neutron structures of the Helicobacter pylori 5'-methylthioadenosine nucleosidase highlight proton sharing and protonation states.

Banco, M.T.Mishra, V.Ostermann, A.Schrader, T.E.Evans, G.B.Kovalevsky, A.Ronning, D.R.

(2016) Proc. Natl. Acad. Sci. U.S.A. 113: 13756-13761

  • DOI: 10.1073/pnas.1609718113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • MTAN (5'-methylthioadenosine nucleosidase) catalyzes the hydrolysis of the N-ribosidic bond of a variety of adenosine-containing metabolites. The Helicobacter pylori MTAN (HpMTAN) hydrolyzes 6-amino-6-deoxyfutalosine in the second step of the alterna ...

    MTAN (5'-methylthioadenosine nucleosidase) catalyzes the hydrolysis of the N-ribosidic bond of a variety of adenosine-containing metabolites. The Helicobacter pylori MTAN (HpMTAN) hydrolyzes 6-amino-6-deoxyfutalosine in the second step of the alternative menaquinone biosynthetic pathway. Substrate binding of the adenine moiety is mediated almost exclusively by hydrogen bonds, and the proposed catalytic mechanism requires multiple proton-transfer events. Of particular interest is the protonation state of residue D198, which possesses a pK a above 8 and functions as a general acid to initiate the enzymatic reaction. In this study we present three corefined neutron/X-ray crystal structures of wild-type HpMTAN cocrystallized with S-adenosylhomocysteine (SAH), Formycin A (FMA), and (3R,4S)-4-(4-Chlorophenylthiomethyl)-1-[(9-deaza-adenin-9-yl)methyl]-3-hydroxypyrrolidine (p-ClPh-Thio-DADMe-ImmA) as well as one neutron/X-ray crystal structure of an inactive variant (HpMTAN-D198N) cocrystallized with SAH. These results support a mechanism of D198 pKa elevation through the unexpected sharing of a proton with atom N7 of the adenine moiety possessing unconventional hydrogen-bond geometry. Additionally, the neutron structures also highlight active site features that promote the stabilization of the transition state and slight variations in these interactions that result in 100-fold difference in binding affinities between the DADMe-ImmA and ImmA analogs.


    Organizational Affiliation

    Heinz Maier-Leibnitz Zentrum, Technische Universität München, 85748 Garching, Germany.,Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606; donald.ronning@utoledo.edu.,Ferrier Research Institute, Victoria University of Wellington, Wellington 5010, New Zealand.,Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831.,Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606.,Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, 85747 Garching, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aminodeoxyfutalosine nucleosidase
A
229Helicobacter 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
4CT
Query on 4CT

Download SDF File 
Download CCD File 
A
(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-chlorophenyl)sulfanyl]methyl}pyrrolidin-3-ol
C18 H20 Cl N5 O S
MZZBHZOHYGEGEE-DOMZBBRYSA-N
 Ligand Interaction
DOD
Query on DOD

Download SDF File 
Download CCD File 
A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4CTKd: 0.6 nM (94) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.253 
  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.205 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 83.189α = 90.00
b = 83.189β = 90.00
c = 67.633γ = 120.00
Software Package:
Software NamePurpose
REFMACphasing
SCALAdata scaling
nCNSrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Database references