4me6
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 4me6 is ON HOLD Authors: Doan, T.N.T., Kim, J.K., Ahn, Y.J., Lee, B.M., Kang, L.W. Description: Crystal structure of D-alanine-D-alanine ligase A f...) |
|||
| (6 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP== | |
| + | <StructureSection load='4me6' size='340' side='right'caption='[[4me6]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[4me6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_oryzae_pv._oryzae_KACC_10331 Xanthomonas oryzae pv. oryzae KACC 10331]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ME6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ME6 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]] 2.1Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4me6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4me6 OCA], [https://pdbe.org/4me6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4me6 RCSB], [https://www.ebi.ac.uk/pdbsum/4me6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4me6 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/Q5H614_XANOR Q5H614_XANOR] Cell wall formation (By similarity).[SAAS:SAAS005905_004_000867][HAMAP-Rule:MF_00047] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | d-Alanine-d-alanine ligase (DDL) catalyzes the biosynthesis of d-alanyl-d-alanine, an essential bacterial peptidoglycan precursor, and is an important drug target for the development of antibacterials. We determined four different crystal structures of DDL from Xanthomonas oryzae pv. oryzae (Xoo) causing Bacteria Blight (BB), which include apo, ADP-bound, ATP-bound, and AMPPNP-bound structures at the resolution between 2.3 and 2.0 A. Similarly with other DDLs, the active site of XoDDL is formed by three loops from three domains at the center of enzyme. Compared with d-alanyl-d-alanine and ATP-bound TtDDL structure, the gamma-phosphate of ATP in XoDDL structure was shifted outside toward solution. We swapped the omega-loop (loop3) of XoDDL with those of Escherichia coli and Helicobacter pylori DDLs, and measured the enzymatic kinetics of wild-type XoDDL and two mutant XoDDLs with the swapped omega-loops. Results showed that the direct interactions between omega-loop and other two loops are essential for the active ATP conformation for D-ala-phosphate formation. | ||
| - | + | Crystal structures of d-alanine-d-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides.,Doan TT, Kim JK, Ngo HP, Tran HT, Cha SS, Min Chung K, Huynh KH, Ahn YJ, Kang LW Arch Biochem Biophys. 2014 Jan 16;545C:92-99. doi: 10.1016/j.abb.2014.01.009. PMID:24440607<ref>PMID:24440607</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 4me6" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[D-alanine-D-alanine ligase 3D structures|D-alanine-D-alanine ligase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Xanthomonas oryzae pv. oryzae KACC 10331]] | ||
| + | [[Category: Ahn YJ]] | ||
| + | [[Category: Doan TTN]] | ||
| + | [[Category: Kang LW]] | ||
| + | [[Category: Kim JK]] | ||
| + | [[Category: Lee BM]] | ||
Current revision
Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP
| |||||||||||
