4oa4: Difference between revisions
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==CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SHEWANELLA LOIHICA PV-4 (Shew_1446), TARGET EFI-510273, WITH BOUND SUCCINATE== | ==CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SHEWANELLA LOIHICA PV-4 (Shew_1446), TARGET EFI-510273, WITH BOUND SUCCINATE== | ||
<StructureSection load='4oa4' size='340' side='right' caption='[[4oa4]], [[Resolution|resolution]] 1.60Å' scene=''> | <StructureSection load='4oa4' size='340' side='right'caption='[[4oa4]], [[Resolution|resolution]] 1.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4oa4]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4oa4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_loihica_PV-4 Shewanella loihica PV-4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OA4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OA4 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand= | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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=4oa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oa4 OCA], [https://pdbe.org/4oa4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oa4 RCSB], [https://www.ebi.ac.uk/pdbsum/4oa4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oa4 ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/DCTP_SHELP DCTP_SHELP] Part of the tripartite ATP-independent periplasmic (TRAP) transport system DctPQM involved in C4-dicarboxylates uptake (By similarity). Required for the utilization of succinate, fumarate, L-malate and alpha-ketoglutarate (PubMed:29769716). Binds succinate and malate (PubMed:25540822).[UniProtKB:Q9HU18]<ref>PMID:25540822</ref> <ref>PMID:29769716</ref> | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 18: | Line 18: | ||
</div> | </div> | ||
<div class="pdbe-citations 4oa4" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 4oa4" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[TRAP dicarboxylate transporter%2C DctP subunit|TRAP dicarboxylate transporter%2C DctP subunit]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Shewanella loihica PV-4]] | ||
[[Category: | [[Category: Al Obaidi NF]] | ||
[[Category: | [[Category: Almo SC]] | ||
[[Category: | [[Category: Attonito JD]] | ||
[[Category: | [[Category: Chowdhury S]] | ||
[[Category: | [[Category: Evans B]] | ||
[[Category: | [[Category: Gerlt JA]] | ||
[[Category: Hillerich | [[Category: Hillerich B]] | ||
[[Category: Imker | [[Category: Imker HJ]] | ||
[[Category: Love | [[Category: Love J]] | ||
[[Category: Morisco | [[Category: Morisco LL]] | ||
[[Category: | [[Category: Scott Glenn A]] | ||
[[Category: Seidel | [[Category: Seidel RD]] | ||
[[Category: Sojitra | [[Category: Sojitra S]] | ||
[[Category: Stead | [[Category: Stead M]] | ||
[[Category: Vetting | [[Category: Vetting MW]] | ||
[[Category: Wasserman | [[Category: Wasserman SR]] | ||
Revision as of 10:13, 25 January 2023
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SHEWANELLA LOIHICA PV-4 (Shew_1446), TARGET EFI-510273, WITH BOUND SUCCINATECRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SHEWANELLA LOIHICA PV-4 (Shew_1446), TARGET EFI-510273, WITH BOUND SUCCINATE
Structural highlights
FunctionDCTP_SHELP Part of the tripartite ATP-independent periplasmic (TRAP) transport system DctPQM involved in C4-dicarboxylates uptake (By similarity). Required for the utilization of succinate, fumarate, L-malate and alpha-ketoglutarate (PubMed:29769716). Binds succinate and malate (PubMed:25540822).[UniProtKB:Q9HU18][1] [2] Publication Abstract from PubMedThe rate at which genome sequencing data is accruing demands enhanced methods for functional annotation and metabolism discovery. Solute binding proteins (SBPs) facilitate the transport of the first reactant in a metabolic pathway, thereby constraining the regions of chemical space and the chemistries that must be considered for pathway reconstruction. We describe high-throughput protein production and differential scanning fluorimetry platforms, which enabled the screening of 158 SBPs against a 189 component library specifically tailored for this class of proteins. Like all screening efforts, this approach is limited by the practical constraints imposed by construction of the library, i.e., we can study only those metabolites that are known to exist and which can be made in sufficient quantities for experimentation. To move beyond these inherent limitations, we illustrate the promise of crystallographic- and mass spectrometric-based approaches for the unbiased use of entire metabolomes as screening libraries. Together, our approaches identified 40 new SBP ligands, generated experiment-based annotations for 2084 SBPs in 71 isofunctional clusters, and defined numerous metabolic pathways, including novel catabolic pathways for the utilization of ethanolamine as sole nitrogen source and the use of d-Ala-d-Ala as sole carbon source. These efforts begin to define an integrated strategy for realizing the full value of amassing genome sequence data. Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.,Vetting MW, Al-Obaidi N, Zhao S, San Francisco B, Kim J, Wichelecki DJ, Bouvier JT, Solbiati JO, Vu H, Zhang X, Rodionov DA, Love JD, Hillerich BS, Seidel RD, Quinn RJ, Osterman AL, Cronan JE, Jacobson MP, Gerlt JA, Almo SC Biochemistry. 2015 Jan 27;54(3):909-31. doi: 10.1021/bi501388y. Epub 2015 Jan 16. PMID:25540822[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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