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| | <StructureSection load='5dmx' size='340' side='right'caption='[[5dmx]], [[Resolution|resolution]] 2.81Å' scene=''> | | <StructureSection load='5dmx' size='340' side='right'caption='[[5dmx]], [[Resolution|resolution]] 2.81Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5dmx]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Acibc Acibc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DMX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5dmx]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii_ACICU Acinetobacter baumannii ACICU]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DMX FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ddl, ACICU_03532 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=405416 ACIBC])</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]] 2.81Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-alanine--D-alanine_ligase D-alanine--D-alanine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.4 6.3.2.4] </span></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=5dmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmx OCA], [https://pdbe.org/5dmx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dmx RCSB], [https://www.ebi.ac.uk/pdbsum/5dmx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dmx 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=5dmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dmx OCA], [http://pdbe.org/5dmx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dmx RCSB], [http://www.ebi.ac.uk/pdbsum/5dmx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dmx ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DDL_ACIBC DDL_ACIBC]] Cell wall formation.[HAMAP-Rule:MF_00047] | + | [https://www.uniprot.org/uniprot/DDL_ACIBC DDL_ACIBC] Cell wall formation.[HAMAP-Rule:MF_00047] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Acibc]] | + | [[Category: Acinetobacter baumannii ACICU]] |
| - | [[Category: D-alanine--D-alanine ligase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Hong, M K]] | + | [[Category: Hong MK]] |
| - | [[Category: Huynh, K H]] | + | [[Category: Huynh KH]] |
| - | [[Category: Kang, L W]] | + | [[Category: Kang LW]] |
| - | [[Category: Acinetobacter baumannii]]
| + | |
| - | [[Category: Apo structure]]
| + | |
| - | [[Category: D-alanine-d-alanine ligase]]
| + | |
| - | [[Category: Drug target protein]]
| + | |
| - | [[Category: Ligase]]
| + | |
| Structural highlights
Function
DDL_ACIBC Cell wall formation.[HAMAP-Rule:MF_00047]
Publication Abstract from PubMed
Acinetobacter baumannii, which is emerging as a multidrug-resistant nosocomial pathogen, causes a number of diseases, including pneumonia, bacteremia, meningitis, and skin infections. With ATP hydrolysis, the D-alanine-D-alanine ligase (DDL) catalyzes the synthesis of D-alanyl-D-alanine, which is an essential component of bacterial peptidoglycan. In this study, we determined the crystal structure of DDL from A. baumannii (AbDDL) at a resolution of 2.2 A. The asymmetric unit contained six protomers of AbDDL. Five protomers had a closed conformation in the central domain, while one protomer had an open conformation in the central domain. The central domain with an open conformation did not interact with crystallographic symmetry-related protomers and the conformational change of the central domain was not due to crystal packing. The central domain of AbDDL can have an ensemble of the open and closed conformations before the binding of substrate ATP. The conformational change of the central domain is important for the catalytic activity and the detail information will be useful for the development of inhibitors against AbDDL and putative antibacterial agents against A. baumannii. The AbDDL structure was compared with that of other DDLs that were in complex with potent inhibitors and the catalytic activity of AbDDL was confirmed using enzyme kinetics assays.
The crystal structure of the D-alanine-D-alanine ligase from Acinetobacter baumannii suggests a flexible conformational change in the central domain before nucleotide binding.,Huynh KH, Hong MK, Lee C, Tran HT, Lee SH, Ahn YJ, Cha SS, Kang LW J Microbiol. 2015 Nov;53(11):776-82. doi: 10.1007/s12275-015-5475-8. Epub 2015, Oct 28. PMID:26502962[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Huynh KH, Hong MK, Lee C, Tran HT, Lee SH, Ahn YJ, Cha SS, Kang LW. The crystal structure of the D-alanine-D-alanine ligase from Acinetobacter baumannii suggests a flexible conformational change in the central domain before nucleotide binding. J Microbiol. 2015 Nov;53(11):776-82. doi: 10.1007/s12275-015-5475-8. Epub 2015, Oct 28. PMID:26502962 doi:http://dx.doi.org/10.1007/s12275-015-5475-8
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