4FFS

Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Helicobacter pylori with butyl-thio-DADMe-Immucillin-A

• PDB DOI: https://doi.org/10.2210/pdb4FFS/pdb

• Classification: HYDROLASE
• Organism(s): Helicobacter pylori J99
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-06-01 Released: 2012-09-26 
• Deposition Author(s): Haapalainen, A.M., Rinaldo-Matthis, A., Brown, R.L., Norris, G.E., Almo, S.C., Schramm, V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.192 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 

Literature

A Picomolar Transition State Analogue Inhibitor of MTAN as a Specific Antibiotic for Helicobacter pylori.

Wang, S., Haapalainen, A.M., Yan, F., Du, Q., Tyler, P.C., Evans, G.B., Rinaldo-Matthis, A., Brown, R.L., Norris, G.E., Almo, S.C., Schramm, V.L.

(2012) Biochemistry 51: 6892-6894

• PubMed: 22891633 
• DOI: https://doi.org/10.1021/bi3009664
• Primary Citation of Related Structures:  
  4FFS


• PubMed Abstract: 
  

  Campylobacter and Helicobacter species express a 6-amino-6-deoxyfutalosine N-ribosylhydrolase (HpMTAN) proposed to function in menaquinone synthesis. BuT-DADMe-ImmA is a 36 pM transition state analogue of HpMTAN, and the crystal structure of the enzyme-inhibitor complex reveals the mechanism of inhibition. BuT-DADMe-ImmA has a MIC(90) value of <8 ng/mL for Helicobacter pylori growth but does not cause growth arrest in other common clinical pathogens, thus demonstrating potential as an H. pylori-specific antibiotic.

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Organizational Affiliation: 

Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 26.66 kDa 
• Atom Count: 2,071 
• Modelled Residue Count: 232 
• Deposited Residue Count: 239 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MTA/SAH nucleosidase	A	239	Helicobacter pylori J99	Mutation(s): 0  Gene Names: jhp_0082, mtn, mtnN, Pfs EC: 3.2.2.9 (PDB Primary Data), 3.2.2.30 (UniProt)
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
BIG	B [auth A]	(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(butylsulfanyl)methyl]pyrrolidin-3-ol C16 H25 N5 O S LTSUEVPGSXUJHT-OLZOCXBDSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
BIG	PDBBind:  4FFS	Kd: 0.04 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.192 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 
• Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.732	α = 90
b = 157.732	β = 90
c = 157.732	γ = 90

Software Package:

Software Name	Purpose
XDisplayF	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-26 
Deposition Author(s): Haapalainen, A.M., Rinaldo-Matthis, A., Brown, R.L., Norris, G.E., Almo, S.C., Schramm, V.L.

Revision History  

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations