4J83

SET7/9 in complex with TAF10K189A peptide and AdoMet


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases.

Horowitz, S.Dirk, L.M.Yesselman, J.D.Nimtz, J.S.Adhikari, U.Mehl, R.A.Scheiner, S.Houtz, R.L.Al-Hashimi, H.M.Trievel, R.C.

(2013) J.Am.Chem.Soc. 135: 15536-15548

  • DOI: 10.1021/ja407140k
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • S-adenosylmethionine (AdoMet)-based methylation is integral to metabolism and signaling. AdoMet-dependent methyltransferases belong to multiple distinct classes and share a catalytic mechanism that arose through convergent evolution; however, fundame ...

    S-adenosylmethionine (AdoMet)-based methylation is integral to metabolism and signaling. AdoMet-dependent methyltransferases belong to multiple distinct classes and share a catalytic mechanism that arose through convergent evolution; however, fundamental determinants underlying this shared methyl transfer mechanism remain undefined. A survey of high-resolution crystal structures reveals that unconventional carbon-oxygen (CH···O) hydrogen bonds coordinate the AdoMet methyl group in different methyltransferases irrespective of their class, active site structure, or cofactor binding conformation. Corroborating these observations, quantum chemistry calculations demonstrate that these charged interactions formed by the AdoMet sulfonium cation are stronger than typical CH···O hydrogen bonds. Biochemical and structural studies using a model lysine methyltransferase and an active site mutant that abolishes CH···O hydrogen bonding to AdoMet illustrate that these interactions are important for high-affinity AdoMet binding and transition-state stabilization. Further, crystallographic and NMR dynamics experiments of the wild-type enzyme demonstrate that the CH···O hydrogen bonds constrain the motion of the AdoMet methyl group, potentially facilitating its alignment during catalysis. Collectively, the experimental findings with the model methyltransferase and structural survey imply that methyl CH···O hydrogen bonding represents a convergent evolutionary feature of AdoMet-dependent methyltransferases, mediating a universal mechanism for methyl transfer.


    Organizational Affiliation

    Howard Hughes Medical Institute , Ann Arbor, Michigan 48109, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase SETD7
A
261Homo sapiensMutation(s): 0 
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
11Homo sapiensMutation(s): 1 
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
SAM
Query on SAM

Download SDF File 
Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
B
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.188 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 83.475α = 90.00
b = 83.475β = 90.00
c = 95.785γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-08
    Type: Initial release
  • Version 1.1: 2014-05-07
    Type: Other