|
|
| (One intermediate revision not shown.) |
| Line 3: |
Line 3: |
| | <StructureSection load='4p3l' size='340' side='right'caption='[[4p3l]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='4p3l' size='340' side='right'caption='[[4p3l]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4p3l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Chrsd Chrsd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P3L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4P3L FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4p3l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chromohalobacter_salexigens_DSM_3043 Chromohalobacter salexigens DSM 3043]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P3L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4P3L FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BDP:BETA-D-GLUCOPYRANURONIC+ACID'>BDP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.8Å</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=BDP:BETA-D-GLUCOPYRANURONIC+ACID'>BDP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Csal_2479 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=290398 CHRSD])</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=4p3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p3l OCA], [https://pdbe.org/4p3l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4p3l RCSB], [https://www.ebi.ac.uk/pdbsum/4p3l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4p3l 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=4p3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p3l OCA], [http://pdbe.org/4p3l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4p3l RCSB], [http://www.ebi.ac.uk/pdbsum/4p3l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4p3l ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/DCTP_CHRSD DCTP_CHRSD] Solute-binding protein that binds D-glucuronate (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 == |
| Line 18: |
Line 19: |
| | </div> | | </div> |
| | <div class="pdbe-citations 4p3l" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4p3l" 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: Chrsd]] | + | [[Category: Chromohalobacter salexigens DSM 3043]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[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_CHRSD Solute-binding protein that binds D-glucuronate (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
|
