5JPC

Joint X-ray/neutron structure of MTAN complex with Formycin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.208 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.282 

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 pKa 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

    Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606.




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
FMC
Query on FMC

Download SDF File 
Download CCD File 
A
(1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol
C10 H13 N5 O4
KBHMEHLJSZMEMI-KSYZLYKTSA-N
 Ligand Interaction
DOD
Query on DOD

Download SDF File 
Download CCD File 
A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.208 
  • 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
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.282 
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACphasing
HKL-3000data reduction
nCNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Space - XUnited States--

Revision History 

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