3LGS

A. thaliana MTA nucleosidase in complex with S-adenosylhomocysteine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanism of substrate specificity in 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidases.

Siu, K.K.Asmus, K.Zhang, A.N.Horvatin, C.Li, S.Liu, T.Moffatt, B.Woods, V.L.Howell, P.L.

(2011) J.Struct.Biol. 173: 86-98

  • DOI: 10.1016/j.jsb.2010.06.006

  • PubMed Abstract: 
  • 5'-Methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN) plays a key role in the methionine-recycling pathway of bacteria and plants. Despite extensive structural and biochemical studies, the molecular mechanism of substrate specif ...

    5'-Methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN) plays a key role in the methionine-recycling pathway of bacteria and plants. Despite extensive structural and biochemical studies, the molecular mechanism of substrate specificity for MTAN remains an outstanding question. Bacterial MTANs show comparable efficiency in hydrolyzing MTA and SAH, while the plant enzymes select preferentially for MTA, with either no or significantly reduced activity towards SAH. Bacterial and plant MTANs show significant conservation in the overall structure, and the adenine- and ribose-binding sites. The observation of a more constricted 5'-alkylthio binding site in Arabidopsis thalianaAtMTAN1 and AtMTAN2, two plant MTAN homologues, led to the hypothesis that steric hindrance may play a role in substrate selection in plant MTANs. We show using isothermal titration calorimetry that SAH binds to both Escherichia coli MTAN (EcMTAN) and AtMTAN1 with comparable micromolar affinity. To understand why AtMTAN1 can bind but not hydrolyze SAH, we determined the structure of the protein-SAH complex at 2.2Å resolution. The lack of catalytic activity appears to be related to the enzyme's inability to bind the substrate in a catalytically competent manner. The role of dynamics in substrate selection was also examined by probing the amide proton exchange rates of EcMTAN and AtMTAN1 via deuterium-hydrogen exchange coupled mass spectrometry. These results correlate with the B factors of available structures and the thermodynamic parameters associated with substrate binding, and suggest a higher level of conformational flexibility in the active site of EcMTAN. Our results implicate dynamics as an important factor in substrate selection in MTAN.


    Related Citations: 
    • Molecular determinants of substrate specificity in plant 5'-methylthioadenosine nucleosidases.
      Siu, K.K.,Lee, J.E.,Sufrin, J.R.,Moffatt, B.A.,McMillan, M.,Cornell, K.A.,Isom, C.,Howell, P.L.
      (2008) J.Mol.Biol. 378: 112


    Organizational Affiliation

    Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-methylthioadenosine nucleosidases
A, B, C, D
267Arabidopsis thalianaMutation(s): 0 
Gene Names: MTN1 (MTAN, MTAN1)
EC: 3.2.2.9
Find proteins for Q9T0I8 (Arabidopsis thaliana)
Go to UniProtKB:  Q9T0I8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B, C, D
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
ADE
Query on ADE

Download SDF File 
Download CCD File 
A, B, C, D
ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ADEKd: 1700 nM BINDINGMOAD
SAHKd: 24800 nM BINDINGMOAD
SAHKd: 24800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.850α = 90.00
b = 126.410β = 101.73
c = 83.810γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
PHASERphasing
CrystalCleardata collection
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance