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==Crystal structure of a trap periplasmic solute binding protein from Bordetella bronchispeptica (bb3421), target EFI-510039, with density modeled as pantoate==
==Crystal structure of a trap periplasmic solute binding protein from Bordetella bronchispeptica (bb3421), target EFI-510039, with density modeled as pantoate==
<StructureSection load='4nq8' size='340' side='right' caption='[[4nq8]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
<StructureSection load='4nq8' size='340' side='right'caption='[[4nq8]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4nq8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_bronchisepticus Alcaligenes bronchisepticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NQ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NQ8 FirstGlance]. <br>
<table><tr><td colspan='2'>[[4nq8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bordetella_bronchiseptica_RB50 Bordetella bronchiseptica RB50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NQ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NQ8 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PAF:PANTOATE'>PAF</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]] 1.5&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BB3421 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=257310 Alcaligenes bronchisepticus])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PAF:PANTOATE'>PAF</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=4nq8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nq8 OCA], [http://pdbe.org/4nq8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nq8 RCSB], [http://www.ebi.ac.uk/pdbsum/4nq8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nq8 ProSAT]</span></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=4nq8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nq8 OCA], [https://pdbe.org/4nq8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nq8 RCSB], [https://www.ebi.ac.uk/pdbsum/4nq8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nq8 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/A0A0H3LPK2_BORBR A0A0H3LPK2_BORBR]
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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4nq8" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Alcaligenes bronchisepticus]]
[[Category: Bordetella bronchiseptica RB50]]
[[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: Imker, H J]]
[[Category: Imker HJ]]
[[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: Vetting, M W]]
[[Category: Vetting MW]]
[[Category: Wasserman, S R]]
[[Category: Wasserman SR]]
[[Category: Efi]]
[[Category: Enzyme function initiative]]
[[Category: Protein transport]]
[[Category: Structural genomic]]
[[Category: Trap periplasmic solute binding family]]

Latest revision as of 15:34, 1 March 2024

Crystal structure of a trap periplasmic solute binding protein from Bordetella bronchispeptica (bb3421), target EFI-510039, with density modeled as pantoateCrystal structure of a trap periplasmic solute binding protein from Bordetella bronchispeptica (bb3421), target EFI-510039, with density modeled as pantoate

Structural highlights

4nq8 is a 2 chain structure with sequence from Bordetella bronchiseptica RB50. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.5Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A0H3LPK2_BORBR

4nq8, resolution 1.50Å

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OCA
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