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| | ==CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM ROSEOBACTER DENITRIFICANS OCh 114 (RD1_1052, TARGET EFI-510238) WITH BOUND L-GALACTONATE== | | ==CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM ROSEOBACTER DENITRIFICANS OCh 114 (RD1_1052, TARGET EFI-510238) WITH BOUND L-GALACTONATE== |
| - | <StructureSection load='4pcd' size='340' side='right' caption='[[4pcd]], [[Resolution|resolution]] 1.70Å' scene=''> | + | <StructureSection load='4pcd' size='340' side='right'caption='[[4pcd]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4pcd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Erythrobacter_sp._(strain_och_114) Erythrobacter sp. (strain och 114)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PCD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PCD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4pcd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Roseobacter_denitrificans_OCh_114 Roseobacter denitrificans OCh 114]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PCD FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2Q2:L-GALACTONIC+ACID'>2Q2</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]] 1.7Å</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2Q2:L-GALACTONIC+ACID'>2Q2</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RD1_1052 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375451 Erythrobacter sp. (strain OCh 114)])</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=4pcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pcd OCA], [https://pdbe.org/4pcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pcd RCSB], [https://www.ebi.ac.uk/pdbsum/4pcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pcd 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=4pcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pcd OCA], [http://pdbe.org/4pcd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4pcd RCSB], [http://www.ebi.ac.uk/pdbsum/4pcd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4pcd ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/DCTP_ROSDO DCTP_ROSDO] Solute-binding protein that binds L-galactonate and D-mannonate (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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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Almo, S C]] | + | [[Category: Large Structures]] |
| - | [[Category: Attonito, J D]] | + | [[Category: Roseobacter denitrificans OCh 114]] |
| - | [[Category: Chowdhury, S]] | + | [[Category: Al Obaidi NF]] |
| - | [[Category: EFI, Enzyme Function Initiative]] | + | [[Category: Almo SC]] |
| - | [[Category: Evans, B]] | + | [[Category: Attonito JD]] |
| - | [[Category: Gerlt, J A]] | + | [[Category: Chowdhury S]] |
| - | [[Category: Glenn, A Scott]] | + | [[Category: Evans B]] |
| - | [[Category: Hillerich, B]] | + | [[Category: Gerlt JA]] |
| - | [[Category: Love, J]] | + | [[Category: Hillerich B]] |
| - | [[Category: Morisco, L L]] | + | [[Category: Love J]] |
| - | [[Category: Obaidi, N F.Al]] | + | [[Category: Morisco LL]] |
| - | [[Category: Seidel, R D]] | + | [[Category: Scott Glenn A]] |
| - | [[Category: Stead, M]] | + | [[Category: Seidel RD]] |
| - | [[Category: Vetting, M W]] | + | [[Category: Stead M]] |
| - | [[Category: Wasserman, S R]] | + | [[Category: Vetting MW]] |
| - | [[Category: Whalen, K L]] | + | [[Category: Wasserman SR]] |
| - | [[Category: Efi]]
| + | [[Category: Whalen KL]] |
| - | [[Category: Enzyme function initiative]]
| + | |
| - | [[Category: Solute-binding protein]]
| + | |
| - | [[Category: Structural genomic]]
| + | |
| - | [[Category: Trap periplasmic solute binding family]]
| + | |
| Structural highlights
Function
DCTP_ROSDO Solute-binding protein that binds L-galactonate and D-mannonate (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.
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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