5EX3

Crystal structure of human SMYD3 in complex with a VEGFR1 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.408 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for Substrate Preference of SMYD3, a SET Domain-containing Protein Lysine Methyltransferase

Fu, W.Liu, N.Qiao, Q.Wang, M.Min, J.Zhu, B.Xu, R.M.Yang, N.

(2016) J.Biol.Chem. 291: 9173-9180

  • DOI: 10.1074/jbc.M115.709832
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • SMYD3 is a SET domain-containing N-lysine methyltransferase associated with multiple cancers. Its reported substrates include histones (H3K4 and H4K5), vascular endothelial growth factor receptor 1 (VEGFR1 Lys(831)) and MAP3 kinase kinase (MAP3K2 Lys ...

    SMYD3 is a SET domain-containing N-lysine methyltransferase associated with multiple cancers. Its reported substrates include histones (H3K4 and H4K5), vascular endothelial growth factor receptor 1 (VEGFR1 Lys(831)) and MAP3 kinase kinase (MAP3K2 Lys(260)). To reveal the structural basis for substrate preference and the catalytic mechanism of SMYD3, we have solved its co-crystal structures with VEGFR1 and MAP3K2 peptides. Our structural and biochemical analyses show that MAP3K2 serves as a robust substrate of SMYD3 because of the presence of a phenylalanine residue at the -2 position. A shallow hydrophobic pocket on SMYD3 accommodates the binding of the phenylalanine and promotes efficient catalytic activities of SMYD3. By contrast, SMYD3 displayed a weak activity toward a VEGFR1 peptide, and the location of the acceptor lysine in the folded kinase domain of VEGFR1 requires drastic conformational rearrangements for juxtaposition of the acceptor lysine with the enzymatic active site. Our results clearly revealed structural determinants for the substrate preference of SMYD3 and provided mechanistic insights into lysine methylation of MAP3K2. The knowledge should be useful for the development of SMYD3 inhibitors in the fight against MAP3K2 and Ras-driven cancer.


    Organizational Affiliation

    From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, the University of Chinese Academy of Sciences, Beijing 100049, China, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase SMYD3
A
436Homo sapiensMutation(s): 2 
Gene Names: SMYD3 (ZMYND1, ZNFN3A1)
EC: 2.1.1.43
Find proteins for Q9H7B4 (Homo sapiens)
Go to Gene View: SMYD3
Go to UniProtKB:  Q9H7B4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VEGFR1 peptide
D
9Homo sapiensMutation(s): 0 
Gene Names: FLT1 (FLT, FRT, VEGFR1)
EC: 2.7.10.1
Find proteins for P17948 (Homo sapiens)
Go to Gene View: FLT1
Go to UniProtKB:  P17948
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
D
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.408 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.378α = 90.00
b = 104.659β = 90.00
c = 117.599γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MOSTChina2015CB856200
National Natural Science Foundation of ChinaChina31521002
National Natural Science Foundation of ChinaChina31430018
National Natural Science Foundation of ChinaChina31210103914
Strategic priority research program of CASChinaXDB08010100
National key new drug creation and manufacturing program of ChinaChina2014ZX09507002

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-05-25
    Type: Database references
  • Version 1.2: 2017-10-18
    Type: Author supporting evidence, Database references, Derived calculations