Crystal Structure of the Helicobacter pylori MTAN-D198N mutant with S-Adenosylhomocysteine in the active site

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.130 

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Crystal structures of the Helicobacter pylori MTAN enzyme reveal specific interactions between S-adenosylhomocysteine and the 5'-alkylthio binding subsite.

Mishra, V.Ronning, D.R.

(2012) Biochemistry 51: 9763-9772

  • DOI: https://doi.org/10.1021/bi301221k
  • Primary Citation of Related Structures:  
    4OJT, 4OY3, 4P54

  • PubMed Abstract: 

    The bacterial 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) enzyme is a multifunctional enzyme that catalyzes the hydrolysis of the N-ribosidic bond of at least four different adenosine-based metabolites: S-adenosylhomocysteine (SAH), 5'-methylthioadenosine (MTA), 5'-deoxyadenosine (5'-DOA), and 6-amino-6-deoxyfutalosine. These activities place the enzyme at the hub of seven fundamental bacterial metabolic pathways: S-adenosylmethionine (SAM) utilization, polyamine biosynthesis, the purine salvage pathway, the methionine salvage pathway, the SAM radical pathways, autoinducer-2 biosynthesis, and menaquinone biosynthesis. The last pathway makes MTAN essential for Helicobacter pylori viability. Although structures of various bacterial and plant MTANs have been described, the interactions between the homocysteine moiety of SAH and the 5'-alkylthiol binding site of MTAN have never been resolved. We have determined crystal structures of an inactive mutant form of H. pylori MTAN bound to MTA and SAH to 1.63 and 1.20 Å, respectively. The active form of MTAN was also crystallized in the presence of SAH, allowing the determination of the structure of a ternary enzyme-product complex resolved at 1.50 Å. These structures identify interactions between the homocysteine moiety and the 5'-alkylthiol binding site of the enzyme. This information can be leveraged for the development of species-specific MTAN inhibitors that prevent the growth of H. pylori.

  • Organizational Affiliation

    Department of Chemistry, University of Toledo, Toledo, OH 43606, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminodeoxyfutalosine nucleosidase231Helicobacter pylori J99Mutation(s): 1 
Gene Names: mtnNmtnjhp_0082
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for Q9ZMY2 (Helicobacter pylori (strain J99 / ATCC 700824))
Explore Q9ZMY2 
Go to UniProtKB:  Q9ZMY2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZMY2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SAH

Download Ideal Coordinates CCD File 
C14 H20 N6 O5 S
Query on CL

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.130 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.733α = 90
b = 80.733β = 90
c = 67.199γ = 120
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-17
    Type: Initial release