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 
  • R-Value Observed: 0.122 

Starting Model: experimental
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This is version 1.2 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 U S A 113: 2104

  • DOI: https://doi.org/10.1073/pnas.1510959113
  • Primary Citation of Related Structures:  
    5A19, 5A1G, 5A1I

  • 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 their dysregulation has been tightly linked to liver and colon cancers. We present crystal structures of human MATα2 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-2395Homo sapiensMutation(s): 0 
EC: 2.5.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for P31153 (Homo sapiens)
Explore P31153 
Go to UniProtKB:  P31153
PHAROS:  P31153
GTEx:  ENSG00000168906 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31153
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S7M
Query on S7M

Download Ideal Coordinates CCD File 
F [auth A][(3S)-3-amino-3-carboxypropyl]{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}ethyls ulfonium
C16 H25 N6 O5 S
UBQZUBPODLPCFG-XIFWJBDBSA-O
PPK
Query on PPK

Download Ideal Coordinates CCD File 
D [auth A](DIPHOSPHONO)AMINOPHOSPHONIC ACID
H6 N O9 P3
PELPUMGXMYVGSQ-UHFFFAOYSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
E [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
K
Query on K

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G [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.122 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.39α = 90
b = 94.39β = 90
c = 117.39γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary