5A1G

The structure of Human MAT2A in complex with S-adenosylethionine and PPNP.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.120 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystallography Captures Catalytic Steps in Human Methionine Adenosyltransferase Enzymes.

Murray, B.Antonyuk, S.V.Marina, A.Lu, S.C.Mato, J.M.Hasnain, S.S.Rojas, A.L.

(2016) Proc.Natl.Acad.Sci.USA 113: 2104

  • DOI: 10.1073/pnas.1510959113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The principal methyl donor of the cell, S-adenosylmethionine (SAMe), is produced by the highly conserved family of methionine adenosyltranferases (MATs) via an ATP-driven process. These enzymes play an important role in the preservation of life, and ...

    The principal methyl donor of the cell, S-adenosylmethionine (SAMe), is produced by the highly conserved family of methionine adenosyltranferases (MATs) via an ATP-driven process. These enzymes play an important role in the preservation of life, and their dysregulation has been tightly linked to liver and colon cancers. We present crystal structures of human MATĪ±2 containing various bound ligands, providing a "structural movie" of the catalytic steps. High- to atomic-resolution structures reveal the structural elements of the enzyme involved in utilization of the substrates methionine and adenosine and in formation of the product SAMe. MAT enzymes are also able to produce S-adenosylethionine (SAE) from substrate ethionine. Ethionine, an S-ethyl analog of the amino acid methionine, is known to induce steatosis and pancreatitis. We show that SAE occupies the active site in a manner similar to SAMe, confirming that ethionine also uses the same catalytic site to form the product SAE.


    Organizational Affiliation

    Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, England; Structural Biology Unit, Center for Cooperative Research in Biosciences, 48160 Derio, Spain;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-2
A
395Homo sapiensMutation(s): 0 
Gene Names: MAT2A (AMS2, MATA2)
EC: 2.5.1.6
Find proteins for P31153 (Homo sapiens)
Go to Gene View: MAT2A
Go to UniProtKB:  P31153
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PPK
Query on PPK

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Download CCD File 
A
(DIPHOSPHONO)AMINOPHOSPHONIC ACID
H6 N O9 P3
PELPUMGXMYVGSQ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

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A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
S7M
Query on S7M

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Download CCD File 
A
[(3S)-3-amino-3-carboxypropyl]{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}ethylsulfonium
S-ADENOSYL ETHIONINE
C16 H25 N6 O5 S
UBQZUBPODLPCFG-XIFWJBDBSA-O
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.120 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 68.390α = 90.00
b = 94.390β = 90.00
c = 117.390γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata reduction
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-03-09
    Type: Database references