5v92

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==Pekin duck egg lysozyme isoform III (DEL-III), orthorhombic form==
==Pekin duck egg lysozyme isoform III (DEL-III), orthorhombic form==
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<StructureSection load='5v92' size='340' side='right' caption='[[5v92]], [[Resolution|resolution]] 1.11&Aring;' scene=''>
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<StructureSection load='5v92' size='340' side='right'caption='[[5v92]], [[Resolution|resolution]] 1.11&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5v92]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Anas_platyrhynchos Anas platyrhynchos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V92 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V92 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5v92]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Anas_platyrhynchos Anas platyrhynchos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V92 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V92 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=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.11&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5v8g|5v8g]], [[5v94|5v94]]</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=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=5v92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v92 OCA], [http://pdbe.org/5v92 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v92 RCSB], [http://www.ebi.ac.uk/pdbsum/5v92 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v92 ProSAT]</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=5v92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v92 OCA], [https://pdbe.org/5v92 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v92 RCSB], [https://www.ebi.ac.uk/pdbsum/5v92 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v92 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/U3J0P1_ANAPL U3J0P1_ANAPL]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents.[SAAS:SAAS00858876]
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[https://www.uniprot.org/uniprot/LYSC1_ANAPL LYSC1_ANAPL] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents.
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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Biological chelating molecules called siderophores are used to sequester iron and maintain its ferric state. Bacterial substrate-binding proteins (SBPs) bind iron-siderophore complexes and deliver these complexes to ATP-binding cassette (ABC) transporters for import into the cytoplasm, where the iron can be transferred from the siderophore to catalytic enzymes. In Yersinia pestis, the causative agent of plague, the Yersinia iron-uptake (Yiu) ABC transporter has been shown to improve iron acquisition under iron-chelated conditions. The Yiu transporter has been proposed to be an iron-siderophore transporter; however, the precise siderophore substrate is unknown. Therefore, the precise role of the Yiu transporter in Y. pestis survival remains uncharacterized. To better understand the function of the Yiu transporter, the crystal structure of YiuA (YPO1310/y2875), an SBP which functions to present the iron-siderophore substrate to the transporter for import into the cytoplasm, was determined. The 2.20 and 1.77 A resolution X-ray crystal structures reveal a basic triad binding motif at the YiuA canonical substrate-binding site, indicative of a metal-chelate binding site. Structural alignment and computational docking studies support the function of YiuA in binding chelated metal. Additionally, YiuA contains two mobile helices, helix 5 and helix 10, that undergo 2-3 A shifts across crystal forms and demonstrate structural breathing of the c-clamp architecture. The flexibility in both c-clamp lobes suggest that YiuA substrate transfer resembles the Venus flytrap mechanism that has been proposed for other SBPs.
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Duck egg lysozyme (DEL) is a widely used model antigen owing to its capacity to bind with differential affinity to anti-chicken egg lysozyme antibodies. However, no structures of DEL have so far been reported, and the situation had been complicated by the presence of multiple isoforms and conflicting reports of primary sequence. Here, the structures of two DEL isoforms from the eggs of the commonly used Pekin duck (Anas platyrhynchos) are reported. Using structural analyses in combination with mass spectrometry, non-ambiguous DEL primary sequences are reported. Furthermore, the structures and sequences determined here enable rationalization of the binding affinity of DEL for well documented landmark anti-lysozyme antibodies.
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The crystal structure of the Yersinia pestis iron chaperone YiuA reveals a basic triad binding motif for the chelated metal.,Radka CD, Chen D, DeLucas LJ, Aller SG Acta Crystallogr D Struct Biol. 2017 Nov 1;73(Pt 11):921-939. doi:, 10.1107/S2059798317015236. Epub 2017 Oct 26. PMID:29095164<ref>PMID:29095164</ref>
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Structural basis of antigen recognition: crystal structure of duck egg lysozyme.,Langley DB, Crossett B, Schofield P, Jackson J, Zeraati M, Maltby D, Christie M, Burnett D, Brink R, Goodnow C, Christ D Acta Crystallogr D Struct Biol. 2017 Nov 1;73(Pt 11):910-920. doi:, 10.1107/S2059798317013730. Epub 2017 Oct 25. PMID:29095163<ref>PMID:29095163</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
<div class="pdbe-citations 5v92" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 5v92" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Lysozyme 3D structures|Lysozyme 3D structures]]
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Anas platyrhynchos]]
[[Category: Anas platyrhynchos]]
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[[Category: Christ, D]]
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[[Category: Large Structures]]
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[[Category: Langley, D B]]
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[[Category: Christ D]]
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[[Category: Hydrolase]]
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[[Category: Langley DB]]
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[[Category: Lysozyme]]
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[[Category: N-acetylmuramidase]]
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Current revision

Pekin duck egg lysozyme isoform III (DEL-III), orthorhombic form

PDB ID 5v92

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