This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3opw

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:18, 21 February 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 1: Line 1:
==Crystal Structure of the Rph1 catalytic core==
==Crystal Structure of the Rph1 catalytic core==
-
<StructureSection load='3opw' size='340' side='right' caption='[[3opw]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+
<StructureSection load='3opw' size='340' side='right'caption='[[3opw]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3opw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OPW FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3opw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OPW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OPW FirstGlance]. <br>
-
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3opt|3opt]]</td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RPH1, YER169W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3opw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3opw OCA], [https://pdbe.org/3opw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3opw RCSB], [https://www.ebi.ac.uk/pdbsum/3opw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3opw ProSAT]</span></td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Histone_H3]-lysine-36_demethylase [Histone H3]-lysine-36 demethylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.27 1.14.11.27] </span></td></tr>
+
-
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3opw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3opw OCA], [http://pdbe.org/3opw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3opw RCSB], [http://www.ebi.ac.uk/pdbsum/3opw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3opw ProSAT]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/RPH1_YEAST RPH1_YEAST]] Transcriptional repressor of photolyase PHR1. Recognizes and binds the sequence AG(4) in the upstream repressing sequence of PHR1. Derepresses PHR1 transcription when phosphorylated.<ref>PMID:10523651</ref> <ref>PMID:11809875</ref>
+
[https://www.uniprot.org/uniprot/RPH1_YEAST RPH1_YEAST] Transcriptional repressor of photolyase PHR1. Recognizes and binds the sequence AG(4) in the upstream repressing sequence of PHR1. Derepresses PHR1 transcription when phosphorylated.<ref>PMID:10523651</ref> <ref>PMID:11809875</ref>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
Saccharomyces cerevesiae Rph1 is a histone demethylase orthologous to human JMJD2A that can specifically demethylate tri- and dimethylated Lys36 of histone H3. The catalytic core of Rph1 (c-Rph1) is responsible for the demethylase activity which is essential for the transcription elongation of some actively transcribed genes. We report here the crystal structures of c-Rph1 in apo form and in complex with Ni2+ and alpha-ketoglutarate (alpha-KG). The structure of c-Rph1 is composed of a JmjN domain, a long beta-hairpin, a mixed structural motif, and a JmjC domain. The alpha-KG co-factor forms hydrogen-bonding interactions with the side chains of conserved residues, and the Ni2+ ion at the active site is chelated by conserved residues and the cofactor. Structural comparison of Rph1 with JMJD2A indicates that the substrate-binding cleft of Rph1 is formed with several structural elements of the JmjC domain, the long beta-hairpin, and the mixed structural motif; and the methylated Lys36 of H3 is recognized by several conserved residues of the JmjC domain. In vitro biochemical data show that mutations of the key residues at the catalytic center and in the substrate-binding cleft abolish the demethylase activity. In vivo growth phenotype analyses also demonstrate that these residues are essential for its functional roles in transcription elongation. Taken together, our structural and biological data provide insights into the molecular basis of the histone demethylase activity and the substrate specificity of Rph1.
+
-
 
+
-
Crystal structure of the catalytic core of Saccharomyces cerevesiae histone demethylase Rph1: insights into the substrate specificity and catalytic mechanism.,Chang Y, Wu J, Tong XJ, Zhou JQ, Ding J Biochem J. 2010 Nov 10. PMID:21067515<ref>PMID:21067515</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3opw" style="background-color:#fffaf0;"></div>
+
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Atcc 18824]]
+
[[Category: Large Structures]]
-
[[Category: Chang, Y]]
+
[[Category: Saccharomyces cerevisiae]]
-
[[Category: Ding, J]]
+
[[Category: Chang Y]]
-
[[Category: Tong, X]]
+
[[Category: Ding J]]
-
[[Category: Wu, J]]
+
[[Category: Tong X]]
-
[[Category: Zhou, J]]
+
[[Category: Wu J]]
-
[[Category: Catalytic core]]
+
[[Category: Zhou J]]
-
[[Category: Histone demethylase]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Rph1]]
+

Current revision

Crystal Structure of the Rph1 catalytic core

PDB ID 3opw

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3opw"
Personal tools