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4l1k

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==Crystal structure of D-alanine-D-alnine ligase from Xanthomonas oryzae pv. oryzae with AMPPNP==
==Crystal structure of D-alanine-D-alnine ligase from Xanthomonas oryzae pv. oryzae with AMPPNP==
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<StructureSection load='4l1k' size='340' side='right' caption='[[4l1k]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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<StructureSection load='4l1k' size='340' side='right'caption='[[4l1k]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4l1k]] 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=4L1K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4L1K FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4l1k]] 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=4L1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4L1K FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3e5n|3e5n]], [[3rfc|3rfc]], [[3r5f|3r5f]], [[4me6|4me6]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ddl, ddlA, XOO0352 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=291331 XANOR])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4l1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l1k OCA], [https://pdbe.org/4l1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4l1k RCSB], [https://www.ebi.ac.uk/pdbsum/4l1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4l1k ProSAT]</span></td></tr>
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<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>
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<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=4l1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l1k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4l1k RCSB], [http://www.ebi.ac.uk/pdbsum/4l1k PDBsum]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q5H614_XANOR Q5H614_XANOR] Cell wall formation (By similarity).[SAAS:SAAS005905_004_000867][HAMAP-Rule:MF_00047]
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==See Also==
==See Also==
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*[[D-alanine-D-alanine ligase|D-alanine-D-alanine ligase]]
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*[[D-alanine-D-alanine ligase 3D structures|D-alanine-D-alanine ligase 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: D-alanine--D-alanine ligase]]
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[[Category: Large Structures]]
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[[Category: Xanor]]
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[[Category: Xanthomonas oryzae pv. oryzae KACC 10331]]
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[[Category: Doan, T T.N]]
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[[Category: Doan TTN]]
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[[Category: Kang, L W]]
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[[Category: Kang LW]]
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[[Category: Kim, J K]]
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[[Category: Kim JK]]
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[[Category: Ligase]]
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Current revision

Crystal structure of D-alanine-D-alnine ligase from Xanthomonas oryzae pv. oryzae with AMPPNP

PDB ID 4l1k

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