1O92

Methionine Adenosyltransferase complexed with ADP and a L-methionine analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structures of Methionine Adenosyltransferase Complexed with Substrates and Products Reveal the Methionine-ATP Recognition and Give Insights Into the Catalytic Mechanism

Gonzalez, B.Pajares, M.A.Hermoso, J.A.Guillerm, D.Guillerm, G.Sanz-Aparicio, J.

(2003) J Mol Biol 331: 407

  • DOI: 10.1016/s0022-2836(03)00728-9
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Methionine adenosyltransferases (MATs) are a family of enzymes in charge of synthesising S-adenosylmethionine (SAM), the most important methyl donor present in living organisms. These enzymes use methionine and ATP as reaction substrates, which react ...

    Methionine adenosyltransferases (MATs) are a family of enzymes in charge of synthesising S-adenosylmethionine (SAM), the most important methyl donor present in living organisms. These enzymes use methionine and ATP as reaction substrates, which react in a S(N)2 fashion where the sulphur atom from methionine attacks C5' from ATP while triphosphate chain is cleaved. A MAT liver specific isoenzyme has been detected, which exists in two distinct oligomeric forms, a dimer (MAT III) and a tetramer (MAT I). Our previously reported crystal structure of MAT I complexed with an inhibitor led to the identification of the methionine-binding site. We present here the results obtained from the complex of MAT I with a competitive inhibitor of methionine, (2S,4S)-amino-4,5-epoxypentanoic acid (AEP), which presents the same features at the methionine binding site reported before. We have also analysed several complexes of this enzyme with methionine and ATP and analogues of them, in order to characterise the interaction that is produced between both substrates. The crystal structures of the complexes reveal how the substrates recognise each other at the active site of the enzyme, and suggest a putative binding site for the product SAM. The residues involved in the interactions of substrates and products with MAT have been identified, and the results agree with all the previous data concerning mutagenesis experiments and crystallographic work. Moreover, all the information provided from the analysis of the complexes has allowed us to postulate a catalytic mechanism for this family of enzymes. In particular, we propose a key role for Lys182 in the correct positioning of the substrates, and Asp135(*), in stabilising the sulphonium group formed in the product (SAM).


    Related Citations: 
    • 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

    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
S-ADENOSYLMETHIONINE SYNTHETASEA, B396Rattus norvegicusMutation(s): 0 
Gene Names: Mat1aAms1
EC: 2.5.1.6
Find proteins for P13444 (Rattus norvegicus)
Explore P13444 
Go to UniProtKB:  P13444
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
AMB
Query on AMB

Download CCD File 
A
L-2-AMINO-4-METHOXY-CIS-BUT-3-ENOIC ACID
C5 H9 N O3
HLOPMQJRUIOMJO-SWOZAWMQSA-N
 Ligand Interaction
PO4
Query on PO4

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A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
K
Query on K

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B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AMBKi:  56000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.14α = 90
b = 115.14β = 90
c = 160.45γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-05-30
    Changes: Data collection, Structure summary