3td5: Difference between revisions
No edit summary |
No edit summary |
||
| (5 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
< | ==Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala== | ||
<StructureSection load='3td5' size='340' side='right'caption='[[3td5]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3td5]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TD5 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> | |||
-- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene></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=3td5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3td5 OCA], [https://pdbe.org/3td5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3td5 RCSB], [https://www.ebi.ac.uk/pdbsum/3td5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3td5 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/OMP38_ACIB2 OMP38_ACIB2] Functions as a porin (PubMed:9928952). Induces apoptosis in human cell lines through caspase-dependent and AIF-dependent pathways. Purified Omp38 enters host cell and localizes to the mitochondria, which presumably leads to a release of proapoptotic molecules such as cytochrome c and AIF (apoptosis-inducing factor) (PubMed:16008580). Binds peptidoglycan, contributes to cell wall maintenance (Probable).<ref>PMID:16008580</ref> <ref>PMID:9928952</ref> <ref>PMID:16008580</ref> <ref>PMID:21965596</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The 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<ref>PMID:21965596</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3td5" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
< | |||
[[Category: Acinetobacter baumannii]] | [[Category: Acinetobacter baumannii]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Kim HY]] | ||
[[Category: | [[Category: Lee WC]] | ||
[[Category: | [[Category: Park JS]] | ||
[[Category: | [[Category: Song JH]] | ||
Latest revision as of 20:31, 1 November 2023
Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-AlaCrystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala
Structural highlights
FunctionOMP38_ACIB2 Functions as a porin (PubMed:9928952). Induces apoptosis in human cell lines through caspase-dependent and AIF-dependent pathways. Purified Omp38 enters host cell and localizes to the mitochondria, which presumably leads to a release of proapoptotic molecules such as cytochrome c and AIF (apoptosis-inducing factor) (PubMed:16008580). Binds peptidoglycan, contributes to cell wall maintenance (Probable).[1] [2] [3] [4] 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[5] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
|
| ||||||||||||||||||