4oz6: Difference between revisions
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==Structure of the Branched Intermediate in Protein Splicing== | |||
<StructureSection load='4oz6' size='340' side='right'caption='[[4oz6]], [[Resolution|resolution]] 2.79Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4oz6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_xenopi Mycobacterium xenopi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OZ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OZ6 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.786Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TIH:BETA(2-THIENYL)ALANINE'>TIH</scene></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=4oz6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oz6 OCA], [https://pdbe.org/4oz6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oz6 RCSB], [https://www.ebi.ac.uk/pdbsum/4oz6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oz6 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/GYRA_MYCXE GYRA_MYCXE] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings (By similarity). | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Inteins are autoprocessing domains that cut themselves out of host proteins in a traceless manner. This process, known as protein splicing, involves multiple chemical steps that must be coordinated to ensure fidelity in the process. The committed step in splicing involves attack of a conserved Asn side-chain amide on the adjacent backbone amide, leading to an intein-succinimide product and scission of that peptide bond. This cleavage reaction is stimulated by formation of a branched intermediate in the splicing process. The mechanism by which the Asn side-chain becomes activated as a nucleophile is not understood. Here we solve the crystal structure of an intein trapped in the branched intermediate step in protein splicing. Guided by this structure, we use protein-engineering approaches to show that intein-succinimide formation is critically dependent on a backbone-to-side-chain hydrogen-bond. We propose that this interaction serves to both position the side-chain amide for attack and to activate its nitrogen as a nucleophile. Collectively, these data provide an unprecedented view of an intein poised to carry out the rate-limiting step in protein splicing, shedding light on how a nominally nonnucleophilic group, a primary amide, can become activated in a protein active site. | |||
Structure of the branched intermediate in protein splicing.,Liu Z, Frutos S, Bick MJ, Vila-Perello M, Debelouchina GT, Darst SA, Muir TW Proc Natl Acad Sci U S A. 2014 Apr 28. PMID:24778214<ref>PMID:24778214</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4oz6" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Mycobacterium xenopi]] | |||
[[Category: Bick MJ]] | |||
[[Category: Darst SA]] | |||
[[Category: Debelouchina GT]] | |||
[[Category: Frutos S]] | |||
[[Category: Liu Z]] | |||
[[Category: Muir TW]] | |||
[[Category: Vila-Perello M]] | |||
