3M54

SET7/9 Y305F in complex with TAF10 peptide and AdoHcy


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

SET7/9 catalytic mutants reveal the role of active site water molecules in lysine multiple methylation.

Del Rizzo, P.A.Couture, J.F.Dirk, L.M.Strunk, B.S.Roiko, M.S.Brunzelle, J.S.Houtz, R.L.Trievel, R.C.

(2010) J.Biol.Chem. 285: 31849-31858

  • DOI: 10.1074/jbc.M110.114587
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • SET domain lysine methyltransferases (KMTs) methylate specific lysine residues in histone and non-histone substrates. These enzymes also display product specificity by catalyzing distinct degrees of methylation of the lysine ε-amino group. To elucida ...

    SET domain lysine methyltransferases (KMTs) methylate specific lysine residues in histone and non-histone substrates. These enzymes also display product specificity by catalyzing distinct degrees of methylation of the lysine ε-amino group. To elucidate the molecular mechanism underlying this specificity, we have characterized the Y245A and Y305F mutants of the human KMT SET7/9 (also known as KMT7) that alter its product specificity from a monomethyltransferase to a di- and a trimethyltransferase, respectively. Crystal structures of these mutants in complex with peptides bearing unmodified, mono-, di-, and trimethylated lysines illustrate the roles of active site water molecules in aligning the lysine ε-amino group for methyl transfer with S-adenosylmethionine. Displacement or dissociation of these solvent molecules enlarges the diameter of the active site, accommodating the increasing size of the methylated ε-amino group during successive methyl transfer reactions. Together, these results furnish new insights into the roles of active site water molecules in modulating lysine multiple methylation by SET domain KMTs and provide the first molecular snapshots of the mono-, di-, and trimethyl transfer reactions catalyzed by these enzymes.


    Organizational Affiliation

    Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase SETD7
A
261Homo 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
TAF10 peptide
B
11Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
ACE
Query on ACE
B
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.198 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 83.725α = 90.00
b = 83.725β = 90.00
c = 96.050γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-2000data collection
DENZOdata reduction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-11-14
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description