3jrt: Difference between revisions
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< | ==Structure from the mobile metagenome of V. paracholerae: Integron cassette protein Vpc_cass2== | ||
<StructureSection load='3jrt' size='340' side='right'caption='[[3jrt]], [[Resolution|resolution]] 2.30Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3jrt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_paracholerae Vibrio paracholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JRT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JRT FirstGlance]. <br> | |||
or | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=3jrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jrt OCA], [https://pdbe.org/3jrt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jrt RCSB], [https://www.ebi.ac.uk/pdbsum/3jrt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jrt ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Mobile gene cassettes captured within integron arrays encompass a vast and diverse pool of genetic novelty. In most cases, functional annotation of gene cassettes directly recovered by cassette-PCR is obscured by their characteristically high sequence novelty. This inhibits identification of those specific functions or biological features that might constitute preferential factors for lateral gene transfer via the integron system. A structural genomics approach incorporating x-ray crystallography has been utilised on a selection of cassettes to investigate evolutionary relationships hidden at the sequence level. Gene cassettes were accessed from marine sediments (pristine and contaminated sites), as well as a range of Vibrio spp. We present six crystal structures, a remarkably high proportion of our survey of soluble proteins, which were found to possess novel folds. These entirely new structures are diverse, encompassing all-alpha, alpha+beta and alpha/beta fold classes, and many contain clear binding pocket features for small molecule substrates. The new structures emphasise the large repertoire of protein families encoded within the integron cassette metagenome and which remain to be characterised. Oligomeric association is a notable recurring property common to these new integron-derived proteins. In some cases, the protein-protein contact sites utilised in homomeric assembly could instead form suitable contact points for heterogeneous regulator/activator proteins or domains. Such functional features are ideal for a flexible molecular componentry needed to ensure responsive and adaptive bacterial functions. | |||
Integron gene cassettes: a repository of novel protein folds with distinct interaction sites.,Sureshan V, Deshpande CN, Boucher Y, Koenig JE, Stokes HW, Harrop SJ, Curmi PM, Mabbutt BC PLoS One. 2013;8(1):e52934. doi: 10.1371/journal.pone.0052934. Epub 2013 Jan 18. PMID:23349695<ref>PMID:23349695</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
== | </div> | ||
<div class="pdbe-citations 3jrt" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Vibrio paracholerae]] | [[Category: Vibrio paracholerae]] | ||
[[Category: Boucher | [[Category: Boucher Y]] | ||
[[Category: Cuff | [[Category: Cuff M]] | ||
[[Category: Cui | [[Category: Cui H]] | ||
[[Category: Curmi | [[Category: Curmi PMG]] | ||
[[Category: Deshpande | [[Category: Deshpande C]] | ||
[[Category: Edwards | [[Category: Edwards A]] | ||
[[Category: Harrop | [[Category: Harrop SJ]] | ||
[[Category: Joachimiak | [[Category: Joachimiak A]] | ||
[[Category: Mabbutt BC]] | |||
[[Category: Mabbutt | [[Category: Savchenko A]] | ||
[[Category: Savchenko | [[Category: Stokes HW]] | ||
[[Category: Stokes | [[Category: Sureshan V]] | ||
[[Category: Sureshan | [[Category: Xu X]] | ||
[[Category: Xu | |||
Latest revision as of 04:58, 21 November 2024
Structure from the mobile metagenome of V. paracholerae: Integron cassette protein Vpc_cass2Structure from the mobile metagenome of V. paracholerae: Integron cassette protein Vpc_cass2
Structural highlights
Publication Abstract from PubMedMobile gene cassettes captured within integron arrays encompass a vast and diverse pool of genetic novelty. In most cases, functional annotation of gene cassettes directly recovered by cassette-PCR is obscured by their characteristically high sequence novelty. This inhibits identification of those specific functions or biological features that might constitute preferential factors for lateral gene transfer via the integron system. A structural genomics approach incorporating x-ray crystallography has been utilised on a selection of cassettes to investigate evolutionary relationships hidden at the sequence level. Gene cassettes were accessed from marine sediments (pristine and contaminated sites), as well as a range of Vibrio spp. We present six crystal structures, a remarkably high proportion of our survey of soluble proteins, which were found to possess novel folds. These entirely new structures are diverse, encompassing all-alpha, alpha+beta and alpha/beta fold classes, and many contain clear binding pocket features for small molecule substrates. The new structures emphasise the large repertoire of protein families encoded within the integron cassette metagenome and which remain to be characterised. Oligomeric association is a notable recurring property common to these new integron-derived proteins. In some cases, the protein-protein contact sites utilised in homomeric assembly could instead form suitable contact points for heterogeneous regulator/activator proteins or domains. Such functional features are ideal for a flexible molecular componentry needed to ensure responsive and adaptive bacterial functions. Integron gene cassettes: a repository of novel protein folds with distinct interaction sites.,Sureshan V, Deshpande CN, Boucher Y, Koenig JE, Stokes HW, Harrop SJ, Curmi PM, Mabbutt BC PLoS One. 2013;8(1):e52934. doi: 10.1371/journal.pone.0052934. Epub 2013 Jan 18. PMID:23349695[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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