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| | ==CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM RHODOBACTER SPHAEROIDES (Rsph17029_3541, TARGET EFI-510203), APO OPEN PARTIALLY DISORDERED== | | ==CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM RHODOBACTER SPHAEROIDES (Rsph17029_3541, TARGET EFI-510203), APO OPEN PARTIALLY DISORDERED== |
| - | <StructureSection load='4pfr' size='340' side='right' caption='[[4pfr]], [[Resolution|resolution]] 2.60Å' scene=''> | + | <StructureSection load='4pfr' size='340' side='right'caption='[[4pfr]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4pfr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhos1 Rhos1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PFR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PFR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4pfr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides_ATCC_17029 Cereibacter sphaeroides ATCC 17029]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PFR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PFR FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLT:D-MALATE'>MLT</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]] 2.6Å</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=MLT:D-MALATE'>MLT</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Rsph17029_3541 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=349101 RHOS1])</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=4pfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pfr OCA], [https://pdbe.org/4pfr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pfr RCSB], [https://www.ebi.ac.uk/pdbsum/4pfr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pfr 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=4pfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pfr OCA], [http://pdbe.org/4pfr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4pfr RCSB], [http://www.ebi.ac.uk/pdbsum/4pfr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4pfr ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4pfr" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4pfr" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[TRAP dicarboxylate transporter%2C DctP subunit|TRAP dicarboxylate transporter%2C DctP subunit]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Rhos1]] | + | [[Category: Cereibacter sphaeroides ATCC 17029]] |
| - | [[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: 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: Stead, M]] | + | [[Category: Stead M]] |
| - | [[Category: Vetting, M W]] | + | [[Category: Vetting MW]] |
| - | [[Category: Wasserman, S R]] | + | [[Category: Wasserman SR]] |
| - | [[Category: Whalen, K L]] | + | [[Category: Whalen KL]] |
| - | [[Category: Efi]]
| + | |
| - | [[Category: Enzyme function initiative]]
| + | |
| - | [[Category: Solute-binding protein]]
| + | |
| - | [[Category: Structural genomic]]
| + | |
| - | [[Category: Trap periplasmic solute binding family]]
| + | |
| Structural highlights
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[1]
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
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