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5c1p

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<StructureSection load='5c1p' size='340' side='right'caption='[[5c1p]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
<StructureSection load='5c1p' size='340' side='right'caption='[[5c1p]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5c1p]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C1P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C1P FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5c1p]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C1P 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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.4&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ddl, ddlB, YPO0557, y3624, YP_3627 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5c1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c1p OCA], [https://pdbe.org/5c1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c1p RCSB], [https://www.ebi.ac.uk/pdbsum/5c1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c1p ProSAT]</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=5c1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c1p OCA], [http://pdbe.org/5c1p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c1p RCSB], [http://www.ebi.ac.uk/pdbsum/5c1p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c1p ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/DDL_YERPE DDL_YERPE]] cell wall formation {eco
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[https://www.uniprot.org/uniprot/DDL_YERPE DDL_YERPE] cell wall formation {eco
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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D-Alanyl-D-alanine is an essential precursor of bacterial peptidoglycan and is synthesized by D-alanine-D-alanine ligase (DDL) with hydrolysis of ATP; this reaction makes DDL an important drug target for the development of antibacterial agents. Five crystal structures of DDL from Yersinia pestis (YpDDL) were determined at 1.7-2.5 A resolution: apo, AMP-bound, ADP-bound, adenosine 5'-(beta,gamma-imido)triphosphate-bound, and D-alanyl-D-alanine- and ADP-bound structures. YpDDL consists of three domains, in which four loops, loop 1, loop 2 (the serine loop), loop 3 (the omega-loop) and loop 4, constitute the binding sites for two D-alanine molecules and one ATP molecule. Some of them, especially the serine loop and the omega-loop, show flexible conformations, and the serine loop is mainly responsible for the conformational change in substrate nucleotide phosphates. Enzyme-kinetics assays were carried out for both the D-alanine and ATP substrates and a substrate-binding mechanism was proposed for YpDDL involving conformational changes of the loops.
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Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.,Tran HT, Hong MK, Ngo HP, Huynh KH, Ahn YJ, Wang Z, Kang LW Acta Crystallogr D Struct Biol. 2016 Jan;72(Pt 1):12-21. doi:, 10.1107/S2059798315021671. Epub 2016 Jan 1. PMID:26894530<ref>PMID:26894530</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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<div class="pdbe-citations 5c1p" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[D-alanine-D-alanine ligase 3D structures|D-alanine-D-alanine ligase 3D structures]]
*[[D-alanine-D-alanine ligase 3D structures|D-alanine-D-alanine ligase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: D-alanine--D-alanine ligase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Hong, M K]]
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[[Category: Yersinia pestis]]
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[[Category: Kang, L W]]
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[[Category: Hong MK]]
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[[Category: Ngo, H P.T]]
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[[Category: Kang LW]]
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[[Category: Tran, H T]]
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[[Category: Ngo HPT]]
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[[Category: Bacterial cell wall synthesis]]
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[[Category: Tran HT]]
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[[Category: D-alanine-d-alanine ligase]]
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[[Category: Ddl]]
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[[Category: Drug target]]
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[[Category: Ligase]]
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Current revision

Crystal structure of ADP and D-alanyl-D-alanine complexed D-alanine-D-alanine ligase(DDL) from Yersinia pestis

PDB ID 5c1p

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