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5j1m

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==Crystal structure of Csd1-Csd2 dimer II==
==Crystal structure of Csd1-Csd2 dimer II==
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<StructureSection load='5j1m' size='340' side='right' caption='[[5j1m]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
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<StructureSection load='5j1m' size='340' side='right'caption='[[5j1m]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5j1m]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J1M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J1M FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5j1m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J1M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J1M 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=ZN:ZINC+ION'>ZN</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]] 2.35&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5j1k|5j1k]], [[5j1l|5j1l]]</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=ZN:ZINC+ION'>ZN</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=5j1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j1m OCA], [http://pdbe.org/5j1m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j1m RCSB], [http://www.ebi.ac.uk/pdbsum/5j1m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j1m 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=5j1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j1m OCA], [https://pdbe.org/5j1m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j1m RCSB], [https://www.ebi.ac.uk/pdbsum/5j1m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j1m ProSAT]</span></td></tr>
</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/O26068_HELPY O26068_HELPY]
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Colonization of the human gastric mucosa by Helicobacter pylori requires its high motility, which depends on the helical cell shape. In H. pylori, several genes (csd1, csd2, csd3/hdpA, ccmA, csd4, csd5, and csd6) play key roles in determining the cell shape by alteration of cross-linking or by trimming of peptidoglycan stem peptides. H. pylori Csd1, Csd2, and Csd3/HdpA are M23B metallopeptidase family members and may act as d,d-endopeptidases to cleave the d-Ala4-mDAP3 peptide bond of cross-linked dimer muropeptides. Csd3 functions also as the d,d-carboxypeptidase to cleave the d-Ala4-d-Ala5 bond of the muramyl pentapeptide. To provide a basis for understanding molecular functions of Csd1 and Csd2, we have carried out their structural characterizations. We have discovered that (i) Csd2 exists in monomer-dimer equilibrium and (ii) Csd1 and Csd2 form a heterodimer. We have determined crystal structures of the Csd2121-308 homodimer and the heterodimer between Csd1125-312 and Csd2121-308. Overall structures of Csd1125-312 and Csd2121-308 monomers are similar to each other, consisting of a helical domain and a LytM domain. The helical domains of both Csd1 and Csd2 play a key role in the formation of homodimers or heterodimers. The Csd1 LytM domain contains a catalytic site with a Zn2+ ion, which is coordinated by three conserved ligands and two water molecules, whereas the Csd2 LytM domain has incomplete metal ligands and no metal ion is bound. Structural knowledge of these proteins sheds light on the events that regulate the cell wall in H. pylori.
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Structural Basis of the Heterodimer Formation between Cell Shape-Determining Proteins Csd1 and Csd2 from Helicobacter pylori.,An DR, Im HN, Jang JY, Kim HS, Kim J, Yoon HJ, Hesek D, Lee M, Mobashery S, Kim SJ, Suh SW PLoS One. 2016 Oct 6;11(10):e0164243. doi: 10.1371/journal.pone.0164243., eCollection 2016. PMID:27711177<ref>PMID:27711177</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 5j1m" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: An, D R]]
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[[Category: Helicobacter pylori 26695]]
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[[Category: Suh, S W]]
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[[Category: Large Structures]]
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[[Category: Heterodimer]]
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[[Category: An DR]]
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[[Category: Hydrolase]]
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[[Category: Suh SW]]
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[[Category: M23b family metallopeptidase]]
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Current revision

Crystal structure of Csd1-Csd2 dimer II

PDB ID 5j1m

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