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.

4ng7

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:27, 11 January 2023

Crystal structure of a TRAP periplasmic solute binding protein from Citrobacter koseri (CKO_04899), Target EFI-510094, apo, open structure

Structural highlights

4ng7 is a 1 chain structure with sequence from Citrobacter koseri ATCC BAA-895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A8AR30_CITK8

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.

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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4ng7"

@@ Line 1: / Line 1: @@
 ==Crystal structure of a TRAP periplasmic solute binding protein from Citrobacter koseri (CKO_04899), Target EFI-510094, apo, open structure==
-<StructureSection load='4ng7' size='340' side='right' caption='[[4ng7]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='4ng7' size='340' side='right'caption='[[4ng7]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ng7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Citk8 Citk8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NG7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NG7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ng7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Citrobacter_koseri_ATCC_BAA-895 Citrobacter koseri ATCC BAA-895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NG7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NG7 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CKO_04899 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=290338 CITK8])</td></tr>
+</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=4ng7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ng7 OCA], [https://pdbe.org/4ng7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ng7 RCSB], [https://www.ebi.ac.uk/pdbsum/4ng7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ng7 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=4ng7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ng7 OCA], [http://pdbe.org/4ng7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ng7 RCSB], [http://www.ebi.ac.uk/pdbsum/4ng7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ng7 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A8AR30_CITK8 A8AR30_CITK8]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 21: @@
 __TOC__
 </StructureSection>
-[[Category: Citk8]]
+[[Category: Citrobacter koseri ATCC BAA-895]]
-[[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: Structural genomic]]
-[[Category: Transport protein]]
-[[Category: Trap periplasmic solute binding family]]

4ng7

From Proteopedia

Revision as of 08:27, 11 January 2023

Crystal structure of a TRAP periplasmic solute binding protein from Citrobacter koseri (CKO_04899), Target EFI-510094, apo, open structure

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox