4F1W | pdb_00004f1w

Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with Adenine

• PDB DOI: https://doi.org/10.2210/pdb4F1W/pdb

• Classification: HYDROLASE
• Organism(s): Salmonella enterica subsp. enterica serovar Choleraesuis str. SCSA50
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-05-07 Released: 2013-05-01 
• Deposition Author(s): Haapalainen, A.M., Thomas, K., Bonanno, J.B., Almo, S.C., Schramm, V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 
  0.146 (Depositor), 0.146 (DCC) 
• R-Value Work: 
  0.113 (Depositor), 0.112 (DCC) 
• R-Value Observed: 
  0.115 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with Adenine

Haapalainen, A.M., Thomas, K., Tyler, P.C., Evans, G.B., Almo, S.C., Schramm, V.L.

(2013) Structure 21: 963-974

• PubMed: 23685211 
• DOI: https://doi.org/10.1016/j.str.2013.04.009
• Primary Citation Related Structures: 
  4F1W, 4F2P, 4F2W, 4F3C, 4F3K


• PubMed Abstract: 
  

  Accumulation of 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH) in bacteria disrupts the S-adenosylmethionine pool to alter biological methylations, synthesis of polyamines, and production of quorum-sensing molecules. Bacterial metabolism of MTA and SAH depends on MTA/SAH nucleosidase (MTAN), an enzyme not present in humans and a target for quorum sensing because MTAN activity is essential for synthesis of autoinducer-2 molecules. Crystals of Salmonella enterica MTAN with product and transition state analogs of MTA and SAH explain the structural contacts causing pM binding affinity for the inhibitor and reveal a "water-wire" channel for the catalytic nucleophile. The crystal structure shows an extension of the binding pocket filled with polyethylene glycol. We exploited this discovery by the design and synthesis of tailored modifications of the currently existing transition state analogs to fill this site. This site was not anticipated in MTAN structures. Tailored inhibitors with dissociation constants of 5 to 15 pM are characterized.

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Organizational Affiliation: 
• Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, 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: 54.36 kDa 
• Atom Count: 4,166 
• Modeled Residue Count: 465 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase	A, B	248	Salmonella enterica subsp. enterica serovar Choleraesuis str. SCSA50	Mutation(s): 0  Gene Names: EMBL EFZ04802.1, mtnN, pfs, SCA50_0219, SCH_0207 EC: 3.2.2.9

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	D [auth A], E [auth A], P [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	C [auth A], N [auth B], O [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
ADE	M [auth B]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N
PEG	L [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], Q [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free:  0.146 (Depositor), 0.146 (DCC) 
• R-Value Work:  0.113 (Depositor), 0.112 (DCC) 
• R-Value Observed: 0.115 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.05	α = 90
b = 68.12	β = 90
c = 89.66	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-01 
Deposition Author(s): Haapalainen, A.M., Thomas, K., Bonanno, J.B., Almo, S.C., Schramm, V.L.

Revision History  

• Version 1.0: 2013-05-01
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description