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==Crystal structure of a TRAP periplasmic solute binding protein from Rhodoferax ferrireducens (Rfer_1840), Target EFI-510211, with bound malonate, space group I422== | ==Crystal structure of a TRAP periplasmic solute binding protein from Rhodoferax ferrireducens (Rfer_1840), Target EFI-510211, with bound malonate, space group I422== | ||
<StructureSection load='4mev' size='340' side='right' caption='[[4mev]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='4mev' size='340' side='right'caption='[[4mev]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4mev]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4mev]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodoferax_ferrireducens_T118 Rhodoferax ferrireducens T118]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MEV 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]] 1.8Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</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=4mev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mev OCA], [https://pdbe.org/4mev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mev RCSB], [https://www.ebi.ac.uk/pdbsum/4mev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mev ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/DCTP_ALBFT DCTP_ALBFT] Solute-binding protein that binds malonate (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;"> | |||
== Publication Abstract from PubMed == | |||
The 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<ref>PMID:25540822</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4mev" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[TRAP dicarboxylate transporter%2C DctP subunit|TRAP dicarboxylate transporter%2C DctP subunit]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Rhodoferax ferrireducens T118]] | ||
[[Category: | [[Category: Al Obaidi NF]] | ||
[[Category: | [[Category: Almo SC]] | ||
[[Category: | [[Category: Bhosle R]] | ||
[[Category: | [[Category: Chowdhury S]] | ||
[[Category: | [[Category: Evans B]] | ||
[[Category: | [[Category: Gerlt JA]] | ||
[[Category: Hammonds | [[Category: Hammonds J]] | ||
[[Category: Hillerich | [[Category: Hillerich B]] | ||
[[Category: Imker | [[Category: Imker HJ]] | ||
[[Category: Jacobson | [[Category: Jacobson MP]] | ||
[[Category: Love | [[Category: Love J]] | ||
[[Category: | [[Category: Scott Glenn A]] | ||
[[Category: Seidel | [[Category: Seidel RD]] | ||
[[Category: Stead | [[Category: Stead M]] | ||
[[Category: Toro | [[Category: Toro R]] | ||
[[Category: Vetting | [[Category: Vetting MW]] | ||
[[Category: Washington | [[Category: Washington E]] | ||
[[Category: Zhao | [[Category: Zhao S]] | ||
Latest revision as of 19:36, 20 September 2023
Crystal structure of a TRAP periplasmic solute binding protein from Rhodoferax ferrireducens (Rfer_1840), Target EFI-510211, with bound malonate, space group I422Crystal structure of a TRAP periplasmic solute binding protein from Rhodoferax ferrireducens (Rfer_1840), Target EFI-510211, with bound malonate, space group I422
Structural highlights
FunctionDCTP_ALBFT Solute-binding protein that binds malonate (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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