4pak: Difference between revisions
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==CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM VERMINEPHROBACTER EISENIAE EF01-2 (Veis_3954, TARGET EFI-510324) A NEPHRIDIAL SYMBIONT OF THE EARTHWORM EISENIA FOETIDA, BOUND TO (R)-PANTOIC ACID== | ==CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM VERMINEPHROBACTER EISENIAE EF01-2 (Veis_3954, TARGET EFI-510324) A NEPHRIDIAL SYMBIONT OF THE EARTHWORM EISENIA FOETIDA, BOUND TO (R)-PANTOIC ACID== | ||
<StructureSection load='4pak' size='340' side='right' caption='[[4pak]], [[Resolution|resolution]] 1.20Å' scene=''> | <StructureSection load='4pak' size='340' side='right'caption='[[4pak]], [[Resolution|resolution]] 1.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4pak]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PAK OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[4pak]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Verminephrobacter_eiseniae_EF01-2 Verminephrobacter eiseniae EF01-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PAK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PAK FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.2Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PAF:PANTOATE'>PAF</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4pak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pak OCA], [https://pdbe.org/4pak PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pak RCSB], [https://www.ebi.ac.uk/pdbsum/4pak PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pak ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/DCTP_VEREI DCTP_VEREI] Solute-binding protein that binds (R)-pantoate and D-erythronate (in vitro) (PubMed:25540822). Probably part of a tripartite ATP-independent periplasmic (TRAP) transport system that mediates solute transport into the cytoplasm.<ref>PMID:25540822</ref> | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 17: | Line 19: | ||
</div> | </div> | ||
<div class="pdbe-citations 4pak" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 4pak" 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: Verminephrobacter eiseniae EF01-2]] | ||
[[Category: | [[Category: Al Obaidi NF]] | ||
[[Category: | [[Category: Almo SC]] | ||
[[Category: | [[Category: Attonito JD]] | ||
[[Category: | [[Category: Chowdhury S]] | ||
[[Category: | [[Category: Evans B]] | ||
[[Category: Hillerich | [[Category: Gerlt JA]] | ||
[[Category: Love | [[Category: Hillerich B]] | ||
[[Category: Morisco | [[Category: Love J]] | ||
[[Category: | [[Category: Morisco LL]] | ||
[[Category: Seidel | [[Category: Scott Glenn A]] | ||
[[Category: Stead | [[Category: Seidel RD]] | ||
[[Category: Vetting | [[Category: Stead M]] | ||
[[Category: Wasserman | [[Category: Vetting MW]] | ||
[[Category: Whalen | [[Category: Wasserman SR]] | ||
[[Category: Whalen KL]] | |||
Latest revision as of 03:42, 28 December 2023
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM VERMINEPHROBACTER EISENIAE EF01-2 (Veis_3954, TARGET EFI-510324) A NEPHRIDIAL SYMBIONT OF THE EARTHWORM EISENIA FOETIDA, BOUND TO (R)-PANTOIC ACIDCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM VERMINEPHROBACTER EISENIAE EF01-2 (Veis_3954, TARGET EFI-510324) A NEPHRIDIAL SYMBIONT OF THE EARTHWORM EISENIA FOETIDA, BOUND TO (R)-PANTOIC ACID
Structural highlights
FunctionDCTP_VEREI Solute-binding protein that binds (R)-pantoate and D-erythronate (in vitro) (PubMed:25540822). Probably part of a tripartite ATP-independent periplasmic (TRAP) transport system that mediates solute transport into the cytoplasm.[1] 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[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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