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| | <StructureSection load='4oz6' size='340' side='right'caption='[[4oz6]], [[Resolution|resolution]] 2.79Å' scene=''> | | <StructureSection load='4oz6' size='340' side='right'caption='[[4oz6]], [[Resolution|resolution]] 2.79Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4oz6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_xenopei"_(sic)_schwabacher_1959 "mycobacterium xenopei" (sic) schwabacher 1959]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OZ6 FirstGlance]. <br> | + | <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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><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> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gyrA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1789 "Mycobacterium xenopei" (sic) Schwabacher 1959])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </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=4oz6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oz6 OCA], [http://pdbe.org/4oz6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oz6 RCSB], [http://www.ebi.ac.uk/pdbsum/4oz6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oz6 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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). | + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bick, M J]] | + | [[Category: Mycobacterium xenopi]] |
| - | [[Category: Darst, S A]] | + | [[Category: Bick MJ]] |
| - | [[Category: Debelouchina, G T]] | + | [[Category: Darst SA]] |
| - | [[Category: Frutos, S]] | + | [[Category: Debelouchina GT]] |
| - | [[Category: Liu, Z]] | + | [[Category: Frutos S]] |
| - | [[Category: Muir, T W]] | + | [[Category: Liu Z]] |
| - | [[Category: Vila-Perello, M]] | + | [[Category: Muir TW]] |
| - | [[Category: Intein]]
| + | [[Category: Vila-Perello M]] |
| - | [[Category: Isomerase]]
| + | |
| Structural highlights
Function
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).
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Liu Z, Frutos S, Bick MJ, Vila-Perello M, Debelouchina GT, Darst SA, Muir TW. Structure of the branched intermediate in protein splicing. Proc Natl Acad Sci U S A. 2014 Apr 28. PMID:24778214 doi:http://dx.doi.org/10.1073/pnas.1402942111
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