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| | <StructureSection load='4paf' size='340' side='right'caption='[[4paf]], [[Resolution|resolution]] 1.60Å' scene=''> | | <StructureSection load='4paf' size='340' side='right'caption='[[4paf]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4paf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ruepo Ruepo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PAF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PAF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4paf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ruegeria_pomeroyi_DSS-3 Ruegeria pomeroyi DSS-3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PAF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PAF FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DHB:3,4-DIHYDROXYBENZOIC+ACID'>DHB</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DHB:3,4-DIHYDROXYBENZOIC+ACID'>DHB</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4paf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4paf OCA], [https://pdbe.org/4paf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4paf RCSB], [https://www.ebi.ac.uk/pdbsum/4paf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4paf ProSAT]</span></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4pai|4pai]], [[4pbh|4pbh]]</td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SPO1773 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246200 RUEPO])</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=4paf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4paf OCA], [http://pdbe.org/4paf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4paf RCSB], [http://www.ebi.ac.uk/pdbsum/4paf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4paf ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/DCTP_RUEPO DCTP_RUEPO] Solute-binding protein that binds 3,4-dihydroxybenzoate and 3-hydroxybenzoate (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 == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4paf" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4paf" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[TRAP dicarboxylate transporter%2C DctP subunit|TRAP dicarboxylate transporter%2C DctP subunit]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ruepo]] | + | [[Category: Ruegeria pomeroyi DSS-3]] |
| - | [[Category: Almo, S C]] | + | [[Category: Al Obaidi NF]] |
| - | [[Category: Attonito, J D]] | + | [[Category: Almo SC]] |
| - | [[Category: Chowdhury, S]] | + | [[Category: Attonito JD]] |
| - | [[Category: EFI, Enzyme Function Initiative]] | + | [[Category: Chowdhury S]] |
| - | [[Category: Evans, B]] | + | [[Category: Evans B]] |
| - | [[Category: Gerlt, J A]] | + | [[Category: Gerlt JA]] |
| - | [[Category: Glenn, A Scott]]
| + | [[Category: Hillerich B]] |
| - | [[Category: Hillerich, B]] | + | [[Category: Love J]] |
| - | [[Category: Love, J]] | + | [[Category: Morisco LL]] |
| - | [[Category: Morisco, L L]] | + | [[Category: Scott Glenn A]] |
| - | [[Category: Obaidi, N F.Al]] | + | [[Category: Seidel RD]] |
| - | [[Category: Seidel, R D]] | + | [[Category: Stead M]] |
| - | [[Category: Stead, M]] | + | [[Category: Vetting MW]] |
| - | [[Category: Vetting, M W]] | + | [[Category: Wasserman SR]] |
| - | [[Category: Wasserman, S R]] | + | [[Category: Whalen KL]] |
| - | [[Category: Whalen, K L]] | + | |
| - | [[Category: Efi]]
| + | |
| - | [[Category: Enzyme function initiative]]
| + | |
| - | [[Category: Solute-binding protein]]
| + | |
| - | [[Category: Structural genomic]]
| + | |
| - | [[Category: Trap periplasmic solute binding family]]
| + | |
| Structural highlights
Function
DCTP_RUEPO Solute-binding protein that binds 3,4-dihydroxybenzoate and 3-hydroxybenzoate (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 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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ 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. Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes. Biochemistry. 2015 Jan 27;54(3):909-31. doi: 10.1021/bi501388y. Epub 2015 Jan 16. PMID:25540822 doi:http://dx.doi.org/10.1021/bi501388y
- ↑ 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. Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes. Biochemistry. 2015 Jan 27;54(3):909-31. doi: 10.1021/bi501388y. Epub 2015 Jan 16. PMID:25540822 doi:http://dx.doi.org/10.1021/bi501388y
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