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==Crystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio desulfuricans (Ddes_1525), Target EFI-510107, with bound sn-glycerol-3-phosphate==
==Crystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio desulfuricans (Ddes_1525), Target EFI-510107, with bound sn-glycerol-3-phosphate==
<StructureSection load='4nhb' size='340' side='right' caption='[[4nhb]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='4nhb' size='340' side='right'caption='[[4nhb]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4nhb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desda Desda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NHB FirstGlance]. <br>
<table><tr><td colspan='2'>[[4nhb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_desulfuricans_ATCC_27774 Desulfovibrio desulfuricans ATCC 27774]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NHB FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.902&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Ddes_1525 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=525146 DESDA])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></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=4nhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nhb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nhb RCSB], [http://www.ebi.ac.uk/pdbsum/4nhb PDBsum]</span></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=4nhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nhb OCA], [https://pdbe.org/4nhb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nhb RCSB], [https://www.ebi.ac.uk/pdbsum/4nhb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nhb ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/B8J100_DESDA B8J100_DESDA]
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==See Also==
</div>
*[[TRAP dicarboxylate transporter%2C DctP subunit|TRAP dicarboxylate transporter%2C DctP subunit]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Desda]]
[[Category: Desulfovibrio desulfuricans ATCC 27774]]
[[Category: Almo, S C]]
[[Category: Large Structures]]
[[Category: Attonito, J D]]
[[Category: Al Obaidi NF]]
[[Category: Chowdhury, S]]
[[Category: Almo SC]]
[[Category: EFI, Enzyme Function Initiative]]
[[Category: Attonito JD]]
[[Category: Evans, B]]
[[Category: Chowdhury S]]
[[Category: Gerlt, J A]]
[[Category: Evans B]]
[[Category: Glenn, A Scott]]
[[Category: Gerlt JA]]
[[Category: Hillerich, B]]
[[Category: Hillerich B]]
[[Category: Imker, H J]]
[[Category: Imker HJ]]
[[Category: Love, J]]
[[Category: Love J]]
[[Category: Morisco, L L]]
[[Category: Morisco LL]]
[[Category: Obaidi, N F.Al]]
[[Category: Scott Glenn A]]
[[Category: Seidel, R D]]
[[Category: Seidel RD]]
[[Category: Sojitra, S]]
[[Category: Sojitra S]]
[[Category: Stead, M]]
[[Category: Stead M]]
[[Category: Vetting, M W]]
[[Category: Vetting MW]]
[[Category: Wasserman, S R]]
[[Category: Wasserman SR]]
[[Category: Efi]]
[[Category: Enzyme function initiative]]
[[Category: Structural genomic]]
[[Category: Transport protein]]
[[Category: Trap periplasmic solute binding family]]

Latest revision as of 12:33, 1 March 2024

Crystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio desulfuricans (Ddes_1525), Target EFI-510107, with bound sn-glycerol-3-phosphate

4nhb, resolution 1.90Å

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