2z3y: Difference between revisions

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Revision as of 19:51, 20 March 2008

File:2z3y.jpg

, resolution 2.25Å

Ligands:

Gene:

KIAA0601, LSD1 (Homo sapiens)

Coordinates:

save as pdb, mmCIF, xml

Crystal structure of Lysine-specific demethylase1

OverviewOverview

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.

About this StructureAbout this Structure

2Z3Y is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.

ReferenceReference

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

Page seeded by OCA on Thu Mar 20 18:51:56 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2z3y.jpg|left|200px]]<br /><applet load="2z3y" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:2z3y.jpg|left|200px]]
-caption="2z3y, resolution 2.25&Aring;" />
-'''Crystal structure of Lysine-specific demethylase1'''<br />
+ {{Structure
+|PDB= 2z3y |SIZE=350|CAPTION= <scene name='initialview01'>2z3y</scene>, resolution 2.25&Aring;
+|SITE=
+|LIGAND= <scene name='pdbligand=F2N:'>F2N</scene>
+|ACTIVITY=
+|GENE= KIAA0601, LSD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
+}}
+'''Crystal structure of Lysine-specific demethylase1'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-Z3Y is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=F2N:'>F2N</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z3Y OCA].
+Z3Y is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z3Y OCA].
 ==Reference==
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18039463 18039463]
+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:[http://www.ncbi.nlm.nih.gov/pubmed/18039463 18039463]
 [[Category: Homo sapiens]]
 [[Category: Single protein]]
@@ Line 28: / Line 37: @@
 [[Category: lsd1]]
 [[Category: lysine-specific]]
-[[Category: national project on protein structural and functional analyses]]
+[[Category: national project on protein structural and functional analyse]]
 [[Category: nppsfa]]
 [[Category: nucleosome]]
@@ Line 37: / Line 46: @@
 [[Category: riken structural genomics/proteomics initiative]]
 [[Category: rsgi]]
-[[Category: structural genomics]]
+[[Category: structural genomic]]
 [[Category: transcription]]
 [[Category: transcription regulation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:00:01 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:51:56 2008''