5CCE

Joint X-ray/neutron structure of wild type MTAN complexed with SRH and adenine


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION, X-RAY DIFFRACTION

wwPDB Validation 3D Report Full Report


This is version 1.2 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
5'-Methylthioadenosine Nucleosidase
A
230Helicobacter 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D8U
Query on D8U

Download SDF File 
Download CCD File 
A
deuterium(1+)
D
GPRLSGONYQIRFK-DYCDLGHISA-N
 Ligand Interaction
2WP
Query on 2WP

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Download CCD File 
A
(2S)-2-amino-4-({[(2S,3S,4R,5S)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid
C9 H17 N O6 S
IQFWYNFDWRYSRA-LYNCRYNASA-N
 Ligand Interaction
ADE
Query on ADE

Download SDF File 
Download CCD File 
A
ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-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: NEUTRON DIFFRACTION, X-RAY DIFFRACTION
Software Package:
Software NamePurpose
Cootmodel building
CNSrefinement
HKL-3000data processing
nCNSrefinement
DENZOdata processing
SCALEPACKdata scaling
Omodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Aeronautic Space Administration (NASA, United States)United StatesN-123528-01

Revision History 

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Database references
  • Version 1.2: 2020-01-01
    Type: Author supporting evidence