7W29

Crystal Structure of SETD3-SAH in complex with betaA-Orn73 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.241 

Starting Model: experimental
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Literature

Histidine methyltransferase SETD3 methylates structurally diverse histidine mimics in actin.

Hintzen, J.C.J.Ma, H.Deng, H.Witecka, A.Andersen, S.B.Drozak, J.Guo, H.Qian, P.Li, H.Mecinovic, J.

(2022) Protein Sci 31: e4305-e4305

  • DOI: https://doi.org/10.1002/pro.4305
  • Primary Citation of Related Structures:  
    7W28, 7W29

  • PubMed Abstract: 

    Actin histidine N τ -methylation by histidine methyltransferase SETD3 plays an important role in human biology and diseases. Here, we report integrated synthetic, biocatalytic, biostructural, and computational analyses on human SETD3-catalyzed methylation of actin peptides possessing histidine and its structurally and chemically diverse mimics. Our enzyme assays supported by biostructural analyses demonstrate that SETD3 has a broader substrate scope beyond histidine, including N-nucleophiles on the aromatic and aliphatic side chains. Quantum mechanical/molecular mechanical molecular dynamics and free-energy simulations provide insight into binding geometries and the free energy barrier for the enzymatic methyl transfer to histidine mimics, further supporting experimental data that histidine is the superior SETD3 substrate over its analogs. This work demonstrates that human SETD3 has a potential to catalyze efficient methylation of several histidine mimics, overall providing mechanistic, biocatalytic, and functional insight into actin histidine methylation by SETD3.


  • Organizational Affiliation

    Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 1, N-terminally processedA [auth P]16Homo sapiensMutation(s): 0 
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P60709 (Homo sapiens)
Explore P60709 
Go to UniProtKB:  P60709
PHAROS:  P60709
GTEx:  ENSG00000075624 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60709
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase setd3B [auth A]499Homo sapiensMutation(s): 0 
Gene Names: SETD3
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.85 (UniProt)
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
C [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ORN
Query on ORN
A [auth P]L-PEPTIDE LINKINGC5 H12 N2 O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.241 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.467α = 90
b = 77.668β = 90
c = 112.054γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2022-10-05 
  • Deposition Author(s): Li, H., Ma, H.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description