8T9F

Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1.

Abini-Agbomson, S.Gretarsson, K.Shih, R.M.Hsieh, L.Lou, T.De Ioannes, P.Vasilyev, N.Lee, R.Wang, M.Simon, M.D.Armache, J.P.Nudler, E.Narlikar, G.Liu, S.Lu, C.Armache, K.J.

(2023) Mol Cell 83: 2872-2883.e7

  • DOI: https://doi.org/10.1016/j.molcel.2023.07.020
  • Primary Citation of Related Structures:  
    8T9F, 8THU

  • PubMed Abstract: 

    SUV420H1 di- and tri-methylates histone H4 lysine 20 (H4K20me2/H4K20me3) and plays crucial roles in DNA replication, repair, and heterochromatin formation. It is dysregulated in several cancers. Many of these processes were linked to its catalytic activity. However, deletion and inhibition of SUV420H1 have shown distinct phenotypes, suggesting that the enzyme likely has uncharacterized non-catalytic activities. Our cryoelectron microscopy (cryo-EM), biochemical, biophysical, and cellular analyses reveal how SUV420H1 recognizes its nucleosome substrates, and how histone variant H2A.Z stimulates its catalytic activity. SUV420H1 binding to nucleosomes causes a dramatic detachment of nucleosomal DNA from the histone octamer, which is a non-catalytic activity. We hypothesize that this regulates the accessibility of large macromolecular complexes to chromatin. We show that SUV420H1 can promote chromatin condensation, another non-catalytic activity that we speculate is needed for its heterochromatin functions. Together, our studies uncover and characterize the catalytic and non-catalytic mechanisms of SUV420H1, a key histone methyltransferase that plays an essential role in genomic stability.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase KMT5BA [auth K]393Homo sapiensMutation(s): 0 
Gene Names: KMT5BSUV420H1CGI-85
EC: 2.1.1.362 (PDB Primary Data), 2.1.1.361 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q4FZB7 (Homo sapiens)
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Go to UniProtKB:  Q4FZB7
PHAROS:  Q4FZB7
GTEx:  ENSG00000110066 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4FZB7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4D [auth B],
F
103Xenopus laevisMutation(s): 0 
Gene Names: LOC121398084
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2E [auth A],
I [auth E]
135Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A.ZG,
J [auth C]
128Homo sapiensMutation(s): 0 
Gene Names: H2AZ1H2AFZH2AZ
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Find proteins for P0C0S5 (Homo sapiens)
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GTEx:  ENSG00000164032 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1H,
K [auth D]
123Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (122-MER)B [auth I]146Escherichia coli 'BL21-Gold(DE3)pLysS AG
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (122-MER)C [auth J]146Escherichia coli 'BL21-Gold(DE3)pLysS AG
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM (Subject of Investigation/LOI)
Query on SAM

Download Ideal Coordinates CCD File 
L [auth K]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM115882
The Mark FoundationUnited States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5T32GM088118
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA266978

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-06
    Type: Initial release