1QM4

Methionine Adenosyltransferase Complexed with a L-Methionine Analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The Crystal Structure of Tetrameric Methionine Adenosyltransferase from Rat Liver Reveals the Methionine-Binding Site

Gonzalez, B.Pajares, M.A.Hermoso, J.A.Alvarez, L.Garrido, F.Sufrin, J.R.Sanz-Aparicio, J.

(2000) J.Mol.Biol. 300: 363

  • DOI: 10.1006/jmbi.2000.3858
  • Also Cited By: 1O93, 1O92, 1O90, 1O9T

  • PubMed Abstract: 
  • Most of the transmethylation reactions use the same methyl donor, S-adenosylmethionine (SAM), that is synthesised from methionine and ATP by methionine adenosyltransferase (MAT). In mammals, two MAT enzymes have been detected, one ubiquitous and anot ...

    Most of the transmethylation reactions use the same methyl donor, S-adenosylmethionine (SAM), that is synthesised from methionine and ATP by methionine adenosyltransferase (MAT). In mammals, two MAT enzymes have been detected, one ubiquitous and another liver specific. The liver enzyme exists in two oligomeric forms, a tetramer (MAT I) and a dimer (MAT III), MAT I being the one that shows a higher level of affinity for methionine but a lower SAM synthesis capacity. We have solved the crystal structure of rat liver MAT I at 2.7 A resolution, complexed with a methionine analogue: l-2-amino-4-methoxy-cis-but-3-enoic acid (l-cisAMB). The enzyme consists of four identical subunits arranged in two tight dimers that are related by crystallographic 2-fold symmetry. The crystal structure shows the positions of the relevant cysteine residues in the chain, and that Cys35 and Cys61 are perfectly oriented for forming a disulphide link. This result leads us to propose a hypothesis to explain the control of MAT I/III exchange and hence, the effects observed on activity. We have identified the methionine-binding site into the active-site cavity, for the first time. The l-cisAMB inhibitor is stacked against Phe251 aromatic ring in a rather planar conformation, and its carboxylate group coordinates a Mg(2+), which, in turn, is linked to Asp180. The essential role of the involved residues in MAT activity has been confirmed by site-directed mutagenesis. Phe251 is exposed to solvent and is located in the beginning of the flexible loop Phe251-Ala260 that is connecting the N-terminal domain to the central domain. We postulate that a conformational change may take place during the enzymatic reaction and this is possibly the reason of the unusual two-step mechanism involving tripolyphosphate hydrolysis. Other important mechanistic implications are discussed on the light of the results. Moreover, the critical role that certain residues identified in this study may have in methionine recognition opens further possibilities for rational drug design.


    Related Citations: 
    • Expression of Rat Liver S-Adenosylmethionine Synthetase in Escherichia Coli Results in Two Active Oligomeric Forms
      Alvarez, L.,Mingorance, J.,Pajares, M.A.,Mato, J.M.
      (1994) Biochem.J. 301: 557


    Organizational Affiliation

    Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano CSIC, Serrano 119, 28006 Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METHIONINE ADENOSYLTRANSFERASE, ALPHA FORM
A, B
396Rattus norvegicusMutation(s): 0 
Gene Names: Mat1a (Ams1)
EC: 2.5.1.6
Find proteins for P13444 (Rattus norvegicus)
Go to UniProtKB:  P13444
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
AMB
Query on AMB

Download SDF File 
Download CCD File 
A
L-2-AMINO-4-METHOXY-CIS-BUT-3-ENOIC ACID
C5 H9 N O3
HLOPMQJRUIOMJO-SWOZAWMQSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AMBKi: 56000 nM (99) BINDINGDB
AMBKi: 50000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.230 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 115.200α = 90.00
b = 115.200β = 90.00
c = 159.980γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
MOSFLMdata reduction
AMoREphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-21
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-07-12
    Type: Derived calculations
  • Version 1.4: 2018-05-30
    Type: Data collection, Structure summary