6WK1

SETD3 in Complex with an Actin Peptide with His73 Replaced with Methionine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Characterization of SETD3 methyltransferase-mediated protein methionine methylation.

Dai, S.Holt, M.V.Horton, J.R.Woodcock, C.B.Patel, A.Zhang, X.Young, N.L.Wilkinson, A.W.Cheng, X.

(2020) J Biol Chem 295: 10901-10910

  • DOI: https://doi.org/10.1074/jbc.RA120.014072
  • Primary Citation of Related Structures:  
    6WK1, 6WK2

  • PubMed Abstract: 

    Most characterized protein methylation events encompass arginine and lysine N -methylation, and only a few cases of protein methionine thiomethylation have been reported. Newly discovered oncohistone mutations include lysine-to-methionine substitutions at positions 27 and 36 of histone H3.3. In these instances, the methionine substitution localizes to the active-site pocket of the corresponding histone lysine methyltransferase, thereby inhibiting the respective transmethylation activity. SET domain-containing 3 (SETD3) is a protein ( i.e. actin) histidine methyltransferase. Here, we generated an actin variant in which the histidine target of SETD3 was substituted with methionine. As for previously characterized histone SET domain proteins, the methionine substitution substantially (76-fold) increased binding affinity for SETD3 and inhibited SETD3 activity on histidine. Unexpectedly, SETD3 was active on the substituted methionine, generating S -methylmethionine in the context of actin peptide. The ternary structure of SETD3 in complex with the methionine-containing actin peptide at 1.9 Å resolution revealed that the hydrophobic thioether side chain is packed by the aromatic rings of Tyr 312 and Trp 273 , as well as the hydrocarbon side chain of Ile 310 Our results suggest that placing methionine properly in the active site-within close proximity to and in line with the incoming methyl group of SAM-would allow some SET domain proteins to selectively methylate methionine in proteins.


  • Organizational Affiliation

    Department of Epigenetics and Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 2A [auth Y],
C [auth Z]
23Homo sapiensMutation(s): 1 
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P63261 (Homo sapiens)
Explore P63261 
Go to UniProtKB:  P63261
PHAROS:  P63261
GTEx:  ENSG00000184009 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63261
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-histidine N-methyltransferaseB [auth A],
D [auth B]
594Homo sapiensMutation(s): 0 
Gene Names: SETD3C14orf154
EC: 2.1.1.85
UniProt & NIH Common Fund Data Resources
Find proteins for Q86TU7 (Homo sapiens)
Explore Q86TU7 
Go to UniProtKB:  Q86TU7
PHAROS:  Q86TU7
GTEx:  ENSG00000183576 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86TU7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
G [auth A],
NA [auth B]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth Y]
H [auth A]
I [auth A]
J [auth A]
LA [auth A]
E [auth Y],
H [auth A],
I [auth A],
J [auth A],
LA [auth A],
MA [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth B]
BA [auth A]
BB [auth B]
CA [auth A]
AA [auth A],
AB [auth B],
BA [auth A],
BB [auth B],
CA [auth A],
CB [auth B],
DB [auth B],
EA [auth A],
EB [auth B],
F [auth Y],
FA [auth A],
FB [auth B],
GA [auth A],
GB [auth B],
HA [auth A],
IA [auth A],
JA [auth A],
K [auth A],
KA [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
OA [auth B],
P [auth A],
PA [auth B],
Q [auth A],
QA [auth B],
R [auth A],
RA [auth B],
S [auth A],
SA [auth B],
T [auth A],
TA [auth B],
U [auth A],
UA [auth B],
V [auth A],
VA [auth B],
W [auth A],
WA [auth B],
X [auth A],
XA [auth B],
Y [auth A],
YA [auth B],
Z [auth A],
ZA [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
DA [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.388α = 90
b = 175.531β = 92.359
c = 66.654γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

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 StatesGM049245-23

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description