Biological Assembly 1  

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: 51.51 kDa 
• Atom Count: 3,663 
• Modelled Residue Count: 465 
• Deposited Residue Count: 484 
• Unique protein chains: 1

 1NC3

Crystal structure of E. coli MTA/AdoHcy nucleosidase complexed with formycin A (FMA)

• PDB DOI:  https://doi.org/10.2210/pdb1NC3/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-12-04 Released: 2003-03-25 
• Deposition Author(s): Lee, J.E., Cornell, K.A., Riscoe, M.K., Howell, P.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.247 
• R-Value Work: 0.198 

Literature

Structure of Escherichia coli 5'-methylthioadenosine/ S-adenosylhomocysteine nucleosidase inhibitor complexes provide insight into the conformational changes required for substrate binding and catalysis.

Lee, J.E., Cornell, K.A., Riscoe, M.K., Howell, P.L.

(2003) J Biol Chem 278: 8761-8770

• PubMed: 12496243 
• DOI: https://doi.org/10.1074/jbc.M210836200
• Primary Citation of Related Structures:  
  1NC1, 1NC3


• PubMed Abstract: 
  

5'-Methylthioadenosine/S-adenosylhomocysteine (MTA/AdoHcy) nucleosidase is a key enzyme in a number of critical biological processes in many microbes. This nucleosidase catalyzes the irreversible hydrolysis of the N(9)-C(1') bond of MTA or AdoHcy to form adenine and the corresponding thioribose. The key role of the MTA/AdoHcy nucleosidase in biological methylation, polyamine biosynthesis, methionine recycling, and bacterial quorum sensing has made it an important antimicrobial drug target. The crystal structures of Escherichia coli MTA/AdoHcy nucleosidase complexed with the transition state analog, formycin A (FMA), and the nonhydrolyzable substrate analog, 5'-methylthiotubercidin (MTT) have been solved to 2.2- and 2.0-A resolution, respectively. These are the first MTA/AdoHcy nucleosidase structures to be solved in the presence of inhibitors. These structures clearly identify the residues involved in substrate binding and catalysis in the active site. Comparisons of the inhibitor complexes to the adenine-bound MTA/AdoHcy nucleosidase (Lee, J. E., Cornell, K. A., Riscoe, M. K., and Howell, P. L. (2001) Structure (Camb.) 9, 941-953) structure provide evidence for a ligand-induced conformational change in the active site and the substrate preference of the enzyme. The enzymatic mechanism has been re-examined.

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Organizational Affiliation: 

Structural Biology and Biochemistry, Research Institute, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MTA/SAH nucleosidase	A, B	242	Escherichia coli	Mutation(s): 0  Gene Names: MTN OR PFS OR B0159 OR Z0170 OR ECS0163 EC: 3.2.2.9
UniProt
Find proteins for P0AF12 (Escherichia coli (strain K12)) Explore P0AF12  Go to UniProtKB:  P0AF12

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMC	C [auth A], D [auth B]	(1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol C10 H13 N5 O4 KBHMEHLJSZMEMI-KSYZLYKTSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FMC	PDBBind:  1NC3	Ki: 1.00e+4 (nM) from 1 assay(s)
	Binding MOAD:  1NC3	Ki: 1.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.247 
• R-Value Work: 0.198 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.1	α = 90
b = 69.7	β = 90
c = 127.8	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
d*TREK	data reduction
CNS	refinement
CrystalClear	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-25 
Deposition Author(s): Lee, J.E., Cornell, K.A., Riscoe, M.K., Howell, P.L.

Revision History  

• Version 1.0: 2003-03-25
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance