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.

6pvy

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 06:33, 7 October 2020

E.coli DsbA in complex with benzofuran compound 26 ([6-(3-methoxyphenoxy)-1-benzofuran-3-yl]acetic acid)

Structural highlights

6pvy is a 2 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Gene:	dsbA, dsf, ppfA, b3860, JW3832 (ECOLI)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DSBA_ECOLI] Required for disulfide bond formation in some periplasmic proteins such as PhoA or OmpA. Acts by transferring its disulfide bond to other proteins and is reduced in the process. DsbA is reoxidized by DsbB. Required for pilus biogenesis. PhoP-regulated transcription is redox-sensitive, being activated when the periplasm becomes more reducing (deletion of dsbA/dsbB, treatment with dithiothreitol). MgrB acts between DsbA/DsbB and PhoP/PhoQ in this pathway.^[1] ^[2]

Publication Abstract from PubMed

A fragment-based drug discovery approach was taken to target the thiol-disulfide oxidoreductase enzyme DsbA from Escherichia coli (EcDsbA). This enzyme is critical for the correct folding of virulence factors in many pathogenic Gram-negative bacteria, and small molecule inhibitors can potentially be developed as anti-virulence compounds. Biophysical screening of a library of fragments identified several classes of fragments with affinity to EcDsbA. One hit with high mM affinity, 2-(6-bromobenzofuran-3-yl)acetic acid (6), was chemically elaborated at several positions around the scaffold. X-ray crystal structures of the elaborated analogues showed binding in the hydrophobic binding groove adjacent to the catalytic disulfide bond of EcDsbA. Binding affinity was calculated based on NMR studies and compounds 25 and 28 were identified as the highest affinity binders with dissociation constants (KD) of 326 +/- 25 and 341 +/- 57 microM respectively. This work suggests the potential to develop benzofuran fragments into a novel class of EcDsbA inhibitors.

The Fragment-Based Development of a Benzofuran Hit as a New Class of Escherichia coli DsbA Inhibitors.,Duncan LF, Wang G, Ilyichova OV, Scanlon MJ, Heras B, Abbott BM Molecules. 2019 Oct 18;24(20). pii: molecules24203756. doi:, 10.3390/molecules24203756. PMID:31635355^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Akiyama Y, Kamitani S, Kusukawa N, Ito K. In vitro catalysis of oxidative folding of disulfide-bonded proteins by the Escherichia coli dsbA (ppfA) gene product. J Biol Chem. 1992 Nov 5;267(31):22440-5. PMID:1429594
↑ Lippa AM, Goulian M. Perturbation of the oxidizing environment of the periplasm stimulates the PhoQ/PhoP system in Escherichia coli. J Bacteriol. 2012 Mar;194(6):1457-63. doi: 10.1128/JB.06055-11. Epub 2012 Jan 20. PMID:22267510 doi:http://dx.doi.org/10.1128/JB.06055-11
↑ Duncan LF, Wang G, Ilyichova OV, Scanlon MJ, Heras B, Abbott BM. The Fragment-Based Development of a Benzofuran Hit as a New Class of Escherichia coli DsbA Inhibitors. Molecules. 2019 Oct 18;24(20). pii: molecules24203756. doi:, 10.3390/molecules24203756. PMID:31635355 doi:http://dx.doi.org/10.3390/molecules24203756

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/6pvy"

@@ Line 3: / Line 3: @@
 <StructureSection load='6pvy' size='340' side='right'caption='[[6pvy]], [[Resolution|resolution]] 1.74&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6pvy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PVY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6pvy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PVY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PVY FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=OZG:[6-(3-methoxyphenoxy)-1-benzofuran-3-yl]acetic+acid'>OZG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=OZG:[6-(3-methoxyphenoxy)-1-benzofuran-3-yl]acetic+acid'>OZG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=6pvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pvy OCA], [http://pdbe.org/6pvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pvy RCSB], [http://www.ebi.ac.uk/pdbsum/6pvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pvy ProSAT]</span></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dsbA, dsf, ppfA, b3860, JW3832 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6pvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pvy OCA], [http://pdbe.org/6pvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pvy RCSB], [http://www.ebi.ac.uk/pdbsum/6pvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pvy ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Ecoli]]
 [[Category: Large Structures]]
 [[Category: Heras, B]]

6pvy

From Proteopedia

Revision as of 06:33, 7 October 2020

E.coli DsbA in complex with benzofuran compound 26 ([6-(3-methoxyphenoxy)-1-benzofuran-3-yl]acetic acid)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox