3td3: Difference between revisions
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==Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with glycine== | ==Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with glycine== | ||
<StructureSection load='3td3' size='340' side='right' caption='[[3td3]], [[Resolution|resolution]] 1.59Å' scene=''> | <StructureSection load='3td3' size='340' side='right'caption='[[3td3]], [[Resolution|resolution]] 1.59Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3td3]] is a 8 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3td3]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Aciba Aciba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TD3 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3td4|3td4]], [[3td5|3td5]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3td4|3td4]], [[3td5|3td5]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">omp38 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">omp38 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=470 ACIBA])</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3td3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3td3 OCA], [https://pdbe.org/3td3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3td3 RCSB], [https://www.ebi.ac.uk/pdbsum/3td3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3td3 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[ | [[https://www.uniprot.org/uniprot/OMP38_ACIBA OMP38_ACIBA]] Porin. Induces apoptosis in human laryngeal epithelial HEp-2 cells through caspases-dependent and AIF-dependent pathways. Purified Omp38 enters the cells and localizes to the mitochondria, which leads to a release of proapoptotic molecules such as cytochrome c and AIF (apoptosis-inducing factor).<ref>PMID:16008580</ref> <ref>PMID:9928952</ref> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Aciba]] | [[Category: Aciba]] | ||
[[Category: Large Structures]] | |||
[[Category: Kim, H Y]] | [[Category: Kim, H Y]] | ||
[[Category: Lee, W C]] | [[Category: Lee, W C]] | ||
Revision as of 19:52, 6 July 2022
Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with glycineCrystal structure of OmpA-like domain from Acinetobacter baumannii in complex with glycine
Structural highlights
Function[OMP38_ACIBA] Porin. Induces apoptosis in human laryngeal epithelial HEp-2 cells through caspases-dependent and AIF-dependent pathways. Purified Omp38 enters the cells and localizes to the mitochondria, which leads to a release of proapoptotic molecules such as cytochrome c and AIF (apoptosis-inducing factor).[1] [2] Publication Abstract from PubMedThe outer membrane protein A (OmpA) plays important roles in anchoring of the outer membrane to the bacterial cell wall. The C-terminal periplasmic domain of OmpA (OmpA-like domain) associates with the peptidoglycan (PGN) layer noncovalently. However, there is a paucity of information on the structural aspects of the mechanism of PGN recognition by OmpA-like domains. To elucidate this molecular recognition process, we solved the high-resolution crystal structure of an OmpA-like domain from Acinetobacter baumannii bound to diaminopimelate (DAP), a unique bacterial amino acid from the PGN. The structure clearly illustrates that two absolutely conserved Asp271 and Arg286 residues are the key to the binding to DAP of PGN. Identification of DAP as the central anchoring site of PGN to OmpA is further supported by isothermal titration calorimetry and a pulldown assay with PGN. An NMR-based computational model for complexation between the PGN and OmpA emerged, and this model is validated by determining the crystal structure in complex with a synthetic PGN fragment. These structural data provide a detailed glimpse of how the anchoring of OmpA to the cell wall of gram-negative bacteria takes place in a DAP-dependent manner.-Park, J. S., Lee, W. C., Yeo, K. J., Ryu, K.-S., Kumarasiri, M., Hesek, D., Lee, M., Mobashery, S., Song, J. H., Lim, S. I., Lee, J. C., Cheong, C., Jeon, Y. H., Kim, H.-Y. Mechanism of anchoring of OmpA protein to the cell wall peptidoglycan of the gram-negative bacterial outer membrane. Mechanism of anchoring of OmpA protein to the cell wall peptidoglycan of the gram-negative bacterial outer membrane.,Park JS, Lee WC, Yeo KJ, Ryu KS, Kumarasiri M, Hesek D, Lee M, Mobashery S, Song JH, Kim SI, Lee JC, Cheong C, Jeon YH, Kim HY FASEB J. 2011 Sep 30. PMID:21965596[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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