4YPA

ASH1L SET domain Q2265A mutant in complex with S-adenosyl methionine (SAM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    4YNM, 4YNP, 4YPE, 4YPA, 4YPU

  • 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 blocks access of histone substrate to the enzyme active site ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase ASH1LA, B, C, D226Homo sapiensMutation(s): 1 
Gene Names: ASH1LKIAA1420KMT2H
EC: 2.1.1.43 (PDB Primary Data), 2.1.1 (UniProt), 2.1.1.359 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NR48 (Homo sapiens)
Explore Q9NR48 
Go to UniProtKB:  Q9NR48
PHAROS:  Q9NR48
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM (Subject of Investigation/LOI)
Query on SAM

Download Ideal Coordinates CCD File 
H [auth A], L [auth B], P [auth C], T [auth D]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , I [auth B] , J [auth B] , K [auth B] , M [auth C] , N [auth C] , 
E [auth A],  F [auth A],  G [auth A],  I [auth B],  J [auth B],  K [auth B],  M [auth C],  N [auth C],  O [auth C],  Q [auth D],  R [auth D],  S [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.682α = 91.57
b = 61.773β = 93.83
c = 73.233γ = 90.46
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



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  (Full details and data files)

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