6vdf: Difference between revisions

Latest revision as of 08:09, 11 October 2023

Structure of the periplasmic domain of YejM from Salmonella typhimurium (twinned)

Structural highlights

6vdf is a 4 chain structure with sequence from Salmonella enterica subsp. enterica serovar Typhimurium. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.92Å
Ligands:	EDO, MN, PEG, PGE, PO4, PSE
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

YEJM_SALTY

Publication Abstract from PubMed

Recent recurrent outbreaks of Gram-negative bacteria show the critical need to target essential bacterial mechanisms to fight the increase of antibiotic resistance. Pathogenic Gram-negative bacteria have developed several strategies to protect themselves against the host immune response and antibiotics. One such strategy is to remodel the outer membrane where several genes are involved. yejM was discovered as an essential gene in E. coli and S. typhimurium that plays a critical role in their virulence by changing the outer membrane permeability. How the inner membrane protein YejM with its periplasmic domain changes membrane properties remains unknown. Despite overwhelming structural similarity between the periplasmic domains of two YejM homologues with hydrolases like arylsulfatases, no enzymatic activity has been previously reported for YejM. Our studies reveal an intact active site with bound metal ions in the structure of YejM periplasmic domain. Furthermore, we show that YejM has a phosphatase activity that is dependent on the presence of magnesium ions and is linked to its function of regulating outer membrane properties. Understanding the molecular mechanism by which YejM is involved in outer membrane remodeling will help to identify a new drug target in the fight against the increased antibiotic resistance.

The essential inner membrane protein YejM is a metalloenzyme.,Gabale U, Pena Palomino PA, Kim H, Chen W, Ressl S Sci Rep. 2020 Oct 20;10(1):17794. doi: 10.1038/s41598-020-73660-6. PMID:33082366^[1]

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

References

↑ Gabale U, Pena Palomino PA, Kim H, Chen W, Ressl S. The essential inner membrane protein YejM is a metalloenzyme. Sci Rep. 2020 Oct 20;10(1):17794. doi: 10.1038/s41598-020-73660-6. PMID:33082366 doi:https://dx.doi.org/10.1038/s41598-020-73660-6

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OCA

[1] Gabale U, Pena Palomino PA, Kim H, Chen W, Ressl S. The essential inner membrane protein YejM is a metalloenzyme. Sci Rep. 2020 Oct 20;10(1):17794. doi: 10.1038/s41598-020-73660-6. PMID:33082366 doi:https://dx.doi.org/10.1038/s41598-020-73660-6

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='6vdf' size='340' side='right'caption='[[6vdf]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6vdf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VDF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VDF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6vdf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VDF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PSE:O-PHOSPHOETHANOLAMINE'>PSE</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]] 1.92&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6vat|6vat]], [[6vc7|6vc7]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PSE:O-PHOSPHOETHANOLAMINE'>PSE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pbgA, yejM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</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=6vdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vdf OCA], [https://pdbe.org/6vdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vdf RCSB], [https://www.ebi.ac.uk/pdbsum/6vdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vdf ProSAT]</span></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=6vdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vdf OCA], [http://pdbe.org/6vdf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vdf RCSB], [http://www.ebi.ac.uk/pdbsum/6vdf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vdf ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/YEJM_SALTY YEJM_SALTY]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus typhimurium loeffler 1892]]
 [[Category: Large Structures]]
-[[Category: Gabale, U]]
+[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-[[Category: Ressl, S]]
+[[Category: Gabale U]]
-[[Category: Cardiolipin]]
+[[Category: Ressl S]]
-[[Category: Hydrolase]]
-[[Category: Membrane protein]]
-[[Category: Phosphatase]]
-[[Category: Transport protein]]
-[[Category: Yejm]]

6vdf: Difference between revisions

Latest revision as of 08:09, 11 October 2023

Structure of the periplasmic domain of YejM from Salmonella typhimurium (twinned)

Structural highlights

Function

Publication Abstract from PubMed

References

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