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.


4ypm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
'''Unreleased structure'''
 
-
The entry 4ypm is ON HOLD until Paper Publication
+
==Crystal structure of a LonA protease domain in complex with bortezomib==
 +
<StructureSection load='4ypm' size='340' side='right' caption='[[4ypm]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[4ypm]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YPM FirstGlance]. <br>
 +
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BO2:N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE'>BO2</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
 +
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ypl|4ypl]], [[4ypn|4ypn]]</td></tr>
 +
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_La Endopeptidase La], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.53 3.4.21.53] </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=4ypm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ypm OCA], [http://pdbe.org/4ypm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ypm RCSB], [http://www.ebi.ac.uk/pdbsum/4ypm PDBsum]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[[http://www.uniprot.org/uniprot/A0A059VAZ3_9DEIN A0A059VAZ3_9DEIN]] ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner.[HAMAP-Rule:MF_01973]
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The Lon AAA+ protease (LonA) plays important roles in protein homeostasis and regulation of diverse biological processes. LonA behaves as a homomeric hexamer in the presence of magnesium (Mg(2+)) and performs ATP-dependent proteolysis. However, it is also found that LonA can carry out Mg(2+)-dependent degradation of unfolded protein substrate in an ATP-independent manner. Here we show that in the presence of Mg(2+) LonA forms a non-secluded hexameric barrel with prominent openings, which explains why Mg(2+)-activated LonA can operate as a diffusion-based chambered protease to degrade unstructured protein and peptide substrates efficiently in the absence of ATP. A 1.85 A crystal structure of Mg(2+)-activated protease domain reveals Mg(2+)-dependent remodeling of a substrate-binding loop and a potential metal-binding site near the Ser-Lys catalytic dyad, supported by biophysical binding assays and molecular dynamics simulations. Together, these findings reveal the specific roles of Mg(2+) in the molecular assembly and activation of LonA.
-
Authors: Lin, C.-C., Chang, C.-I.
+
Structural Basis for the Magnesium-Dependent Activation and Hexamerization of the Lon AAA+ Protease.,Su SC, Lin CC, Tai HC, Chang MY, Ho MR, Babu CS, Liao JH, Wu SH, Chang YC, Lim C, Chang CI Structure. 2016 May 3;24(5):676-86. doi: 10.1016/j.str.2016.03.003. Epub 2016 Mar, 31. PMID:27041593<ref>PMID:27041593</ref>
-
Description: Crystal structure of a LonA protease domain in complex with bortezomib
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
[[Category: Unreleased Structures]]
+
</div>
-
[[Category: Lin, C.-C]]
+
<div class="pdbe-citations 4ypm" style="background-color:#fffaf0;"></div>
-
[[Category: Chang, C.-I]]
+
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Endopeptidase La]]
 +
[[Category: Chang, C I]]
 +
[[Category: Lin, C C]]
 +
[[Category: Aaa+ domain]]
 +
[[Category: Bortezomib]]
 +
[[Category: Hydrolase]]
 +
[[Category: Lon protease]]
 +
[[Category: Magnesium]]
 +
[[Category: Protease domain]]

Revision as of 17:49, 10 May 2016

Crystal structure of a LonA protease domain in complex with bortezomib

4ypm, resolution 1.85Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools