8SWA

Crystal structure of the human S-adenosylmethionine synthetase 1 in complex with SAM and PPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.147 

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Ligand Structure Quality Assessment 


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Literature

Formaldehyde regulates S -adenosylmethionine biosynthesis and one-carbon metabolism.

Pham, V.N.Bruemmer, K.J.Toh, J.D.W.Ge, E.J.Tenney, L.Ward, C.C.Dingler, F.A.Millington, C.L.Garcia-Prieto, C.A.Pulos-Holmes, M.C.Ingolia, N.T.Pontel, L.B.Esteller, M.Patel, K.J.Nomura, D.K.Chang, C.J.

(2023) Science 382: eabp9201-eabp9201

  • DOI: https://doi.org/10.1126/science.abp9201
  • Primary Citation of Related Structures:  
    8SWA

  • PubMed Abstract: 

    One-carbon metabolism is an essential branch of cellular metabolism that intersects with epigenetic regulation. In this work, we show how formaldehyde (FA), a one-carbon unit derived from both endogenous sources and environmental exposure, regulates one-carbon metabolism by inhibiting the biosynthesis of S -adenosylmethionine (SAM), the major methyl donor in cells. FA reacts with privileged, hyperreactive cysteine sites in the proteome, including Cys120 in S-adenosylmethionine synthase isoform type-1 (MAT1A). FA exposure inhibited MAT1A activity and decreased SAM production with MAT-isoform specificity. A genetic mouse model of chronic FA overload showed a decrease n SAM and in methylation on selected histones and genes. Epigenetic and transcriptional regulation of Mat1a and related genes function as compensatory mechanisms for FA-dependent SAM depletion, revealing a biochemical feedback cycle between FA and SAM one-carbon units.


  • Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-adenosylmethionine synthase isoform type-1403Homo sapiensMutation(s): 0 
Gene Names: MAT1AAMS1MATA1
EC: 2.5.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for Q00266 (Homo sapiens)
Explore Q00266 
Go to UniProtKB:  Q00266
PHAROS:  Q00266
GTEx:  ENSG00000151224 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00266
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM (Subject of Investigation/LOI)
Query on SAM

Download Ideal Coordinates CCD File 
F [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
PPK
Query on PPK

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

Download Ideal Coordinates CCD File 
E [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.147 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.698α = 90
b = 100.421β = 90
c = 122.74γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release