First time at Proteopedia? Click on the green links: they change the 3D image. Click and drag the molecules. Proteopedia is a 3D, interactive encyclopedia of proteins, RNA, DNA and other molecules. With a free user account, you can edit pages in Proteopedia. Visit the Main Page to learn more.
2dw4
From Proteopedia
| 2dw4, resolution 2.30Å () | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Ligands: | |||||||||
| Domains: | PRK07208, SWIRM, Amino_oxidase, PRK11883 | ||||||||
| |||||||||
| |||||||||
| |||||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB, TOPSAN | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Crystal structure of human LSD1 at 2.3 A resolution
Transcriptional activity and chromatin structure accessibility are correlated with the methylation of specific histone residues. Lysine-specific demethylase 1 (LSD1) is the first discovered histone demethylase, which demethylates Lys4 or Lys9 of histone H3, using FAD. Among the known monoamine oxidase inhibitors, tranylcypromine (Parnate) showed the most potent inhibitory effect on LSD1. Recently, the crystal structure of LSD1 and tranylcypromine was solved at 2.75 A, revealing a five-membered ring fused to the flavin of LSD1. In this study, we refined the crystal structure of the LSD1-tranylcypromine complex to 2.25 A. The five-membered ring model did not fit completely with the electron density, giving R(work)/R(free) values of 0.226/0.254. On the other hand, the N(5) adduct gave the lowest R(work)/R(free) values of 0.218/0.248, among the tested models. These results imply that the LSD1-tranylcypromine complex is not completely composed of the five-membered adduct, but partially contains an intermediate, such as the N(5) adduct.
Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25 A., Mimasu S, Sengoku T, Fukuzawa S, Umehara T, Yokoyama S, Biochem Biophys Res Commun. 2008 Feb 1;366(1):15-22. Epub 2007 Nov 26. PMID:18039463
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
About this Structure
2DW4 is a 1 chain structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
Reference
- Mimasu S, Sengoku T, Fukuzawa S, Umehara T, Yokoyama S. Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25 A. Biochem Biophys Res Commun. 2008 Feb 1;366(1):15-22. Epub 2007 Nov 26. PMID:18039463 doi:10.1016/j.bbrc.2007.11.066
Page seeded by OCA on Tue Feb 17 13:41:20 2009
Categories: Homo sapiens | RSGI, RIKEN Structural Genomics/Proteomics Initiative. | Sengoku, T. | Yokoyama, S. | Amine oxidase | Androgen | Chromatin | Corepressor | Demethylase | Fad | Histone | National project on protein structural and functional analyse | Nppsfa | Oxidoreductase | Riken structural genomics/proteomics initiative | Rsgi | Structural genomic
