5EG2

SET7/9 N265A in complex with AdoHcy and TAF10 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Sulfur-Oxygen Chalcogen Bonding Mediates AdoMet Recognition in the Lysine Methyltransferase SET7/9.

Fick, R.J.Kroner, G.M.Nepal, B.Magnani, R.Horowitz, S.Houtz, R.L.Scheiner, S.Trievel, R.C.

(2016) Acs Chem.Biol. 11: 748-754

  • DOI: 10.1021/acschembio.5b00852

  • PubMed Abstract: 
  • Recent studies have demonstrated that carbon-oxygen (CH···O) hydrogen bonds have important roles in S-adenosylmethionine (AdoMet) recognition and catalysis in methyltransferases. Here, we investigate noncovalent interactions that occur between the Ad ...

    Recent studies have demonstrated that carbon-oxygen (CH···O) hydrogen bonds have important roles in S-adenosylmethionine (AdoMet) recognition and catalysis in methyltransferases. Here, we investigate noncovalent interactions that occur between the AdoMet sulfur cation and oxygen atoms in methyltransferase active sites. These interactions represent sulfur-oxygen (S···O) chalcogen bonds in which the oxygen atom donates a lone pair of electrons to the σ antibonding orbital of the AdoMet sulfur atom. Structural, biochemical, and computational analyses of an asparagine mutation in the lysine methyltransferase SET7/9 that abolishes AdoMet S···O chalcogen bonding reveal that this interaction enhances substrate binding affinity relative to the product S-adenosylhomocysteine. Corroborative quantum mechanical calculations demonstrate that sulfonium systems form strong S···O chalcogen bonds relative to their neutral thioether counterparts. An inspection of high-resolution crystal structures reveals the presence of AdoMet S···O chalcogen bonding in different classes of methyltransferases, illustrating that these interactions are not limited to SET domain methyltransferases. Together, these results demonstrate that S···O chalcogen bonds contribute to AdoMet recognition and can enable methyltransferases to distinguish between substrate and product.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase SETD7
A
262Homo sapiensMutation(s): 1 
Gene Names: SETD7 (KIAA1717, KMT7, SET7, SET9)
EC: 2.1.1.43
Find proteins for Q8WTS6 (Homo sapiens)
Go to Gene View: SETD7
Go to UniProtKB:  Q8WTS6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor TFIID subunit 10
B
10Homo sapiensMutation(s): 0 
Gene Names: TAF10 (TAF2A, TAF2H, TAFII30)
Find proteins for Q12962 (Homo sapiens)
Go to Gene View: TAF10
Go to UniProtKB:  Q12962
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLZ
Query on MLZ
B
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.147 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 83.198α = 90.00
b = 83.198β = 90.00
c = 95.859γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesNSF-CHE-1508492

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-02-03
    Type: Database references
  • Version 1.2: 2016-03-30
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Derived calculations