Crystal structure of E. coli MTA/AdoHcy nucleosidase complexed with 5'-methylthiotubercidin (MTH)

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.190 

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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

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MTA/SAH nucleosidase
A, B
242Escherichia coliMutation(s): 0 
Gene Names: MTN OR PFS OR B0159 OR Z0170 OR ECS0163
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for P0AF12 (Escherichia coli (strain K12))
Explore P0AF12 
Go to UniProtKB:  P0AF12
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AF12
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MTH

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C12 H16 N4 O3 S
Binding Affinity Annotations 
IDSourceBinding Affinity
MTH PDBBind:  1NC1 Ki: 750 (nM) from 1 assay(s)
Binding MOAD:  1NC1 Ki: 750 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.3α = 90
b = 69.3β = 90
c = 127.2γ = 90
Software Package:
Software NamePurpose
CCDSYSdata collection
d*TREKdata reduction
CCDSYSdata reduction
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description