8SWA | pdb_00008swa

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

• PDB DOI: https://doi.org/10.2210/pdb8SWA/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-05-18 Released: 2023-11-15 
• Deposition Author(s): Bruemmer, K.J., Pham, V.N., Toh, J.D.W.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.194 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.143 (Depositor) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

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

• PubMed: 37917677 
• DOI: https://doi.org/10.1126/science.abp9201
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain.
Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain.
Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina.
Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Calle Monforte de Lemos, Madrid, Spain.
Institucio Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluis Companys, Barcelona, Spain.
Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Feixa Llarga, l'Hospitalet de Llobregat, Spain.
Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA.
Innovative Genomics Institute, Berkeley, CA 94704, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 45.58 kDa 
• Atom Count: 3,230 
• Modeled Residue Count: 380 
• Deposited Residue Count: 403 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine synthase isoform type-1	A	403	Homo sapiens	Mutation(s): 0  Gene Names: MAT1A, AMS1, MATA1 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM (Subject of Investigation/LOI)	F [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
PPK	B [auth A]	(DIPHOSPHONO)AMINOPHOSPHONIC ACID H6 N O9 P3 PELPUMGXMYVGSQ-UHFFFAOYSA-N
K	E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	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 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.143 (Depositor) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.698	α = 90
b = 100.421	β = 90
c = 122.74	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-15 
Deposition Author(s): Bruemmer, K.J., Pham, V.N., Toh, J.D.W.

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

Revision History  

• Version 1.0: 2023-11-15
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary