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4mnc

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Crystal structure of a TRAP periplasmic solute binding protein from Polaromonas sp. JS666 (Bpro_4736), Target EFI-510156, with bound benzoyl formate, space group P21

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 ==Crystal structure of a TRAP periplasmic solute binding protein from Polaromonas sp. JS666 (Bpro_4736), Target EFI-510156, with bound benzoyl formate, space group P21==
-<StructureSection load='4mnc' size='340' side='right' caption='[[4mnc]], [[Resolution|resolution]] 1.05&Aring;' scene=''>
+<StructureSection load='4mnc' size='340' side='right'caption='[[4mnc]], [[Resolution|resolution]] 1.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4mnc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Polsj Polsj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MNC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MNC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4mnc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Polaromonas_sp._JS666 Polaromonas sp. JS666]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MNC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MNC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=173:BENZOYL-FORMIC+ACID'>173</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.05&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4mni|4mni]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=173:BENZOYL-FORMIC+ACID'>173</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Bpro_4736 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=296591 POLSJ])</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=4mnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mnc OCA], [https://pdbe.org/4mnc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mnc RCSB], [https://www.ebi.ac.uk/pdbsum/4mnc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mnc ProSAT]</span></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=4mnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mnc OCA], [http://pdbe.org/4mnc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mnc RCSB], [http://www.ebi.ac.uk/pdbsum/4mnc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mnc ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/DCTP2_POLSJ DCTP2_POLSJ] Solute-binding protein that binds phenylglyoxylate (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>
-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>
+==See Also==
+*[[TRAP dicarboxylate transporter%2C DctP subunit|TRAP dicarboxylate transporter%2C DctP subunit]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4mnc" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Polsj]]
+[[Category: Large Structures]]
-[[Category: Almo, S C]]
+[[Category: Polaromonas sp. JS666]]
-[[Category: Bhosle, R]]
+[[Category: Al Obaidi NF]]
-[[Category: Chowdhury, S]]
+[[Category: Almo SC]]
-[[Category: EFI, Enzyme Function Initiative]]
+[[Category: Bhosle R]]
-[[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: Jacobson, M P]]
+[[Category: Jacobson MP]]
-[[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: Toro, R]]
+[[Category: Toro R]]
-[[Category: Vetting, M W]]
+[[Category: Vetting MW]]
-[[Category: Wasserman, S R]]
+[[Category: Wasserman SR]]
-[[Category: Zhao, S]]
+[[Category: Zhao S]]
-[[Category: Efi]]
-[[Category: Enzyme function initiative]]
-[[Category: Structural genomic]]
-[[Category: Transport protein]]
-[[Category: Trap periplasmic solute binding family]]

4mnc

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Current revision

Crystal structure of a TRAP periplasmic solute binding protein from Polaromonas sp. JS666 (Bpro_4736), Target EFI-510156, with bound benzoyl formate, space group P21

Structural highlights

Function

See Also

References

Contents

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