5bpf: Difference between revisions
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New page: '''Unreleased structure''' The entry 5bpf is ON HOLD Authors: Huyen-Thi Tran, Lin-Woo Kang, Myoung-ki Hong Description: Crystal structure of ADP complexed D-alanine-D-alanine ligase(DD... |
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==Crystal structure of ADP complexed D-alanine-D-alanine ligase(DDL) from Yersinia pestis== | |||
<StructureSection load='5bpf' size='340' side='right'caption='[[5bpf]], [[Resolution|resolution]] 2.28Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5bpf]] 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=5BPF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BPF 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]] 2.28Å</td></tr> | |||
<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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5bpf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpf OCA], [https://pdbe.org/5bpf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bpf RCSB], [https://www.ebi.ac.uk/pdbsum/5bpf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bpf ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/DDL_YERPE DDL_YERPE] cell wall formation {eco | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5bpf" 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: Yersinia pestis]] | |||
[[Category: Hong MK]] | |||
[[Category: Kang LW]] | |||
[[Category: Tran HT]] | |||
Latest revision as of 16:05, 8 November 2023
Crystal structure of ADP complexed D-alanine-D-alanine ligase(DDL) from Yersinia pestis
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