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| | ==Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP== | | ==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=''> | + | <StructureSection load='4me6' size='340' side='right'caption='[[4me6]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4me6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Xanor Xanor]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ME6 FirstGlance]. <br> | + | <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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3e5n|3e5n]], [[3r5f|3r5f]], [[4l1k|4l1k]]</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> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ddlA, ddl, XOO0352 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=291331 XANOR])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4me6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4me6 OCA], [http://pdbe.org/4me6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4me6 RCSB], [http://www.ebi.ac.uk/pdbsum/4me6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4me6 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q5H614_XANOR Q5H614_XANOR]] Cell wall formation (By similarity).[SAAS:SAAS005905_004_000867][HAMAP-Rule:MF_00047] | + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[D-alanine-D-alanine ligase|D-alanine-D-alanine ligase]] | + | *[[D-alanine-D-alanine ligase 3D structures|D-alanine-D-alanine ligase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: D-alanine--D-alanine ligase]] | + | [[Category: Large Structures]] |
| - | [[Category: Xanor]] | + | [[Category: Xanthomonas oryzae pv. oryzae KACC 10331]] |
| - | [[Category: Ahn, Y J]] | + | [[Category: Ahn YJ]] |
| - | [[Category: Doan, T T.N]] | + | [[Category: Doan TTN]] |
| - | [[Category: Kang, L W]] | + | [[Category: Kang LW]] |
| - | [[Category: Kim, J K]] | + | [[Category: Kim JK]] |
| - | [[Category: Lee, B M]] | + | [[Category: Lee BM]] |
| - | [[Category: Adp-depending enzyme]]
| + | |
| - | [[Category: D-alanine-d-alanine ligase]]
| + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Nucleotide binding]]
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| Structural highlights
Function
Q5H614_XANOR Cell wall formation (By similarity).[SAAS:SAAS005905_004_000867][HAMAP-Rule:MF_00047]
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Doan TT, Kim JK, Ngo HP, Tran HT, Cha SS, Min Chung K, Huynh KH, Ahn YJ, Kang LW. Crystal structures of d-alanine-d-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides. Arch Biochem Biophys. 2014 Jan 16;545C:92-99. doi: 10.1016/j.abb.2014.01.009. PMID:24440607 doi:http://dx.doi.org/10.1016/j.abb.2014.01.009
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