Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.53 kDa 
• Atom Count: 2269 
• Modelled Residue Count: 230 
• Deposited Residue Count: 231 
• Unique protein chains: 1

4OY3

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

• PDB DOI: 10.2210/pdb4OY3/pdb

• Classification: HYDROLASE
• Organism(s): Helicobacter pylori J99
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-02-10 Released: 2014-12-17 
• Deposition Author(s): Mishra, V., Ronning, D.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.145 
• R-Value Work: 0.130 
• R-Value Observed: 0.130 

Literature

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

• PubMed: 23148563 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminodeoxyfutalosine nucleosidase	A	231	Helicobacter pylori J99	Mutation(s): 1  Gene Names: mtnN, mtn, jhp_0082 EC: 3.2.2.30 (PDB Primary Data), 3.2.2.9 (PDB Primary Data)
UniProt
Find proteins for Q9ZMY2 (Helicobacter pylori (strain J99 / ATCC 700824)) Explore Q9ZMY2  Go to UniProtKB:  Q9ZMY2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 80.733	α = 90
b = 80.733	β = 90
c = 67.199	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-02-10 
• Released Date: 2014-12-17 
Deposition Author(s): Mishra, V., Ronning, D.R.

Revision History  

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