7TD5

Structure of human PRC2-EZH1 containing phosphorylated SUZ12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.196 

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Literature

CK2-mediated phosphorylation of SUZ12 promotes PRC2 function by stabilizing enzyme active site.

Gong, L.Liu, X.Jiao, L.Yang, X.Lemoff, A.Liu, X.

(2022) Nat Commun 13: 6781-6781

  • DOI: https://doi.org/10.1038/s41467-022-34431-1
  • Primary Citation of Related Structures:  
    7TD5

  • PubMed Abstract: 

    Polycomb repressive complex 2 (PRC2) plays a key role in maintaining cell identity during differentiation. Methyltransferase activity of PRC2 on histone H3 lysine 27 is regulated by diverse cellular mechanisms, including posttranslational modification. Here, we report a unique phosphorylation-dependent mechanism stimulating PRC2 enzymatic activity. Residue S583 of SUZ12 is phosphorylated by casein kinase 2 (CK2) in cells. A crystal structure captures phosphorylation in action: the flexible phosphorylation-dependent stimulation loop harboring S583 becomes engaged with the catalytic SET domain through a phosphoserine-centered interaction network, stabilizing the enzyme active site and in particular S-adenosyl-methionine (SAM)-binding pocket. CK2-mediated S583 phosphorylation promotes catalysis by enhancing PRC2 binding to SAM and nucleosomal substrates and facilitates reporter gene repression. Loss of S583 phosphorylation impedes PRC2 recruitment and H3K27me3 deposition in pluripotent mESCs and compromises the ability of PRC2 to maintain differentiated cell identity.


  • Organizational Affiliation

    Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase EZH1
A, F
747Homo sapiensMutation(s): 0 
Gene Names: EZH1KIAA0388
EC: 2.1.1.356
UniProt & NIH Common Fund Data Resources
Find proteins for Q92800 (Homo sapiens)
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Go to UniProtKB:  Q92800
PHAROS:  Q92800
GTEx:  ENSG00000108799 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92800
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein EED
B, G
373Homo sapiensMutation(s): 0 
Gene Names: EED
UniProt & NIH Common Fund Data Resources
Find proteins for O75530 (Homo sapiens)
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PHAROS:  O75530
GTEx:  ENSG00000074266 
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UniProt GroupO75530
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein SUZ12
C, H
179Homo sapiensMutation(s): 0 
Gene Names: SUZ12CHET9JJAZ1KIAA0160
UniProt & NIH Common Fund Data Resources
Find proteins for Q15022 (Homo sapiens)
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PHAROS:  Q15022
GTEx:  ENSG00000178691 
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UniProt GroupQ15022
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
THR-LYS-ALA-ALA-ARG-MET-SER-ALA-PRO-SER
D, I
10Homo sapiensMutation(s): 0 
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Find proteins for P68431 (Homo sapiens)
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PHAROS:  P68431
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
THR-LYS-ALA-ALA-ARG-M3L-SER-ALA-PRO-ALA
E, J
10Homo sapiensMutation(s): 0 
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PHAROS:  P68431
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UniProt GroupP68431
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM (Subject of Investigation/LOI)
Query on SAM

Download Ideal Coordinates CCD File 
BA [auth F],
S [auth A]
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth F]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
AA [auth F],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
T [auth F],
U [auth F],
V [auth F],
W [auth F],
X [auth F],
Y [auth F],
Z [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
C, H
L-PEPTIDE LINKINGC3 H8 N O6 PSER
M3L
Query on M3L
E, J
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 231.87α = 90
b = 64.428β = 109.89
c = 254.496γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
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 General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description