This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


4n6d

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:31, 1 March 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 1: Line 1:
==Crystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio salexigens DSM2638 (Desal_3247), Target EFI-510112, phased with I3C, open complex, C-terminus of symmetry mate bound in ligand binding site==
==Crystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio salexigens DSM2638 (Desal_3247), Target EFI-510112, phased with I3C, open complex, C-terminus of symmetry mate bound in ligand binding site==
-
<StructureSection load='4n6d' size='340' side='right' caption='[[4n6d]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+
<StructureSection load='4n6d' size='340' side='right'caption='[[4n6d]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4n6d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desad Desad]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N6D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4N6D FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4n6d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Maridesulfovibrio_salexigens_DSM_2638 Maridesulfovibrio salexigens DSM 2638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N6D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4N6D 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=I3C:5-AMINO-2,4,6-TRIIODOBENZENE-1,3-DICARBOXYLIC+ACID'>I3C</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]] 1.701&#8491;</td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Desal_3247 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=526222 DESAD])</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=I3C:5-AMINO-2,4,6-TRIIODOBENZENE-1,3-DICARBOXYLIC+ACID'>I3C</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=4n6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n6d OCA], [http://pdbe.org/4n6d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4n6d RCSB], [http://www.ebi.ac.uk/pdbsum/4n6d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4n6d 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=4n6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n6d OCA], [https://pdbe.org/4n6d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4n6d RCSB], [https://www.ebi.ac.uk/pdbsum/4n6d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4n6d ProSAT]</span></td></tr>
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/C6C297_MARSD C6C297_MARSD]
-
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>
+
==See Also==
-
 
+
*[[TRAP dicarboxylate transporter%2C DctP subunit|TRAP dicarboxylate transporter%2C DctP subunit]]
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 4n6d" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Desad]]
+
[[Category: Large Structures]]
-
[[Category: Almo, S C]]
+
[[Category: Maridesulfovibrio salexigens DSM 2638]]
-
[[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: 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: Efi]]
+
-
[[Category: Enzyme function initiative]]
+
-
[[Category: Structural genomic]]
+
-
[[Category: Transport protein]]
+
-
[[Category: Trap periplasmic solute binding family]]
+

Current revision

Crystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio salexigens DSM2638 (Desal_3247), Target EFI-510112, phased with I3C, open complex, C-terminus of symmetry mate bound in ligand binding site

PDB ID 4n6d

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4n6d"
Personal tools