5L3B

Human LSD1/CoREST: LSD1 D556G mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

LSD1/KDM1A mutations associated to a newly described form of intellectual disability impair demethylase activity and binding to transcription factors.

Pilotto, S.Speranzini, V.Marabelli, C.Rusconi, F.Toffolo, E.Grillo, B.Battaglioli, E.Mattevi, A.

(2016) Hum.Mol.Genet. 25: 2578-2587

  • DOI: 10.1093/hmg/ddw120
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Genetic diseases often lead to rare and severe syndromes and the identification of the genetic and protein alterations responsible for the pathogenesis is essential to understand both the physiological and pathological role of the gene product. Recen ...

    Genetic diseases often lead to rare and severe syndromes and the identification of the genetic and protein alterations responsible for the pathogenesis is essential to understand both the physiological and pathological role of the gene product. Recently, de novo variants have been mapped on the gene encoding for the lysine-specific histone demethylase 1 (LSD1)/lysine(K)-specific histone demethylase 1A in three patients characterized by a new genetic disorder. We have analyzed the effects of these pathological mutations on the structure, stability and activity of LSD1 using both in vitro and cellular approaches. The three mutations (Glu403Lys, Asp580Gly and Tyr785His) affect active-site residues and lead to a partial impairment of catalytic activity. They also differentially perturb the ability of LSD1 to engage transcription factors that orchestrate key developmental programs. Moreover, cellular data indicate a decrease in the protein cellular half-life. Taken together, these results demonstrate the relevance of LSD1 in gene regulation and how even moderate alterations in its stability, catalytic activity and binding properties can strongly affect organism development. This depicts a perturbed interplay of catalytic and non-catalytic processes at the origin of the pathology.


    Organizational Affiliation

    Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific histone demethylase 1A
A
852Homo sapiensMutation(s): 1 
Gene Names: KDM1A (AOF2, KDM1, KIAA0601, LSD1)
EC: 1.-.-.-
Find proteins for O60341 (Homo sapiens)
Go to Gene View: KDM1A
Go to UniProtKB:  O60341
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
REST corepressor 1
B
482Homo sapiensMutation(s): 0 
Gene Names: RCOR1 (KIAA0071, RCOR)
Find proteins for Q9UKL0 (Homo sapiens)
Go to Gene View: RCOR1
Go to UniProtKB:  Q9UKL0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.195 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 119.088α = 90.00
b = 179.122β = 90.00
c = 234.411γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
REFMACphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
TelethonItalyGGP12007, GGP14074
AIRCItalyIG:1520
MIURItalyProgetto Bandiera Epigenomica : EPIGEN

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-12-07
    Type: Database references
  • Version 1.2: 2018-04-25
    Type: Data collection