4YPU

ASH1L SET domain K2264L mutant in complex with S-adenosyl methionine (SAM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Two Loops Undergoing Concerted Dynamics Regulate the Activity of the ASH1L Histone Methyltransferase.

Rogawski, D.S.Ndoj, J.Cho, H.J.Maillard, I.Grembecka, J.Cierpicki, T.

(2015) Biochemistry 54: 5401-5413

  • DOI: 10.1021/acs.biochem.5b00697
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ASH1L (absent, small, or homeotic-like 1) is a histone methyltransferase (HMTase) involved in gene activation that is overexpressed in multiple forms of cancer. Previous studies of ASH1L's catalytic SET domain identified an autoinhibitory loop that b ...

    ASH1L (absent, small, or homeotic-like 1) is a histone methyltransferase (HMTase) involved in gene activation that is overexpressed in multiple forms of cancer. Previous studies of ASH1L's catalytic SET domain identified an autoinhibitory loop that blocks access of histone substrate to the enzyme active site. Here, we used both nuclear magnetic resonance and X-ray crystallography to identify conformational dynamics in the ASH1L autoinhibitory loop. Using site-directed mutagenesis, we found that point mutations in the autoinhibitory loop that perturb the structure of the SET domain result in decreased enzyme activity, indicating that the autoinhibitory loop is not a simple gate to the active site but is rather a key feature critical to ASH1L function. We also identified a second loop in the SET-I subdomain of ASH1L that experiences conformational dynamics, and we trapped two different conformations of this loop using crystallographic studies. Mutation of the SET-I loop led to a large decrease in ASH1L enzymatic activity in addition to a significant conformational change in the SET-I loop, demonstrating the importance of the structure and dynamics of the SET-I loop to ASH1L function. Furthermore, we found that three C-terminal chromatin-interacting domains greatly enhance ASH1L enzymatic activity and that ASH1L requires native nucleosome substrate for robust activity. Our study illuminates the role of concerted conformational dynamics in ASH1L function and identifies structural features important for ASH1L enzymatic activity.


    Organizational Affiliation

    Department of Pathology, ‡Center for Stem Cell Biology, Life Sciences Institute, §Division of Hematology-Oncology, Department of Internal Medicine, and ∥Department of Cell and Developmental Biology, University of Michigan , Ann Arbor, Michigan 48109, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase ASH1L
A, B
226Homo sapiensMutation(s): 1 
Gene Names: ASH1L (KIAA1420, KMT2H)
EC: 2.1.1.43
Find proteins for Q9NR48 (Homo sapiens)
Go to Gene View: ASH1L
Go to UniProtKB:  Q9NR48
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A, B
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.238 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 59.108α = 90.00
b = 59.108β = 90.00
c = 226.043γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
MOLREPphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States1R01CA160467
Leukemia & Lymphoma SocietyUnited States6111-14
Leukemia & Lymphoma SocietyUnited States1215-14
American Cancer SocietyUnited StatesRSG-13-130-01-CDD
Michigan Economic Development CorporationUnited States085P1000817
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5T32GM008597
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5T32GM007863

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-09-09
    Type: Database references
  • Version 1.2: 2015-09-16
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2017-10-04
    Type: Author supporting evidence
  • Version 1.5: 2019-12-04
    Type: Author supporting evidence