5y89: Difference between revisions

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 ==Periplasmic heme-binding protein BhuT in complex with one heme (holo-1)==
-<StructureSection load='5y89' size='340' side='right' caption='[[5y89]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='5y89' size='340' side='right'caption='[[5y89]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5y89]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burcj Burcj]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5gj0 5gj0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y89 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y89 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5y89]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_cenocepacia_J2315 Burkholderia cenocepacia J2315]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5gj0 5gj0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y89 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y89 FirstGlance]. <br>
-</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</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>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5giz|5giz]], [[5gj3|5gj3]]</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hmuT, BCAM2628 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216591 BURCJ])</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=5y89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y89 OCA], [https://pdbe.org/5y89 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y89 RCSB], [https://www.ebi.ac.uk/pdbsum/5y89 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y89 ProSAT]</span></td></tr>
-<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=5y89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y89 OCA], [http://pdbe.org/5y89 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y89 RCSB], [http://www.ebi.ac.uk/pdbsum/5y89 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y89 ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/B4EKB3_BURCJ B4EKB3_BURCJ]
-Periplasmic heme-binding proteins (PBPs) in Gram-negative bacteria are components of the heme acquisition system. These proteins shuttle heme across the periplasmic space from outer membrane receptors to ATP-binding cassette (ABC) heme importers located in the inner-membrane. In the present study, we characterized the structures of PBPs found in the pathogen Burkholderia cenocepacia (BhuT) and in the thermophile Roseiflexus sp. RS-1 (RhuT) in the heme-free and heme-bound forms. The conserved motif, in which a well-conserved Tyr interacts with the nearby Arg coordinates on heme iron, was observed in both PBPs. The heme was recognized by its surroundings in a variety of manners including hydrophobic interactions and hydrogen bonds, which was confirmed by isothermal titration calorimetry. Furthermore, this study of 3 forms of BhuT allowed the first structural comparison and showed that the heme-binding cleft of BhuT adopts an "open" state in the heme-free and 2-heme-bound forms, and a "closed" state in the one-heme-bound form with unique conformational changes. Such a conformational change might adjust the interaction of the heme(s) with the residues in PBP and facilitate the transfer of the heme into the translocation channel of the importer.
-Structural basis for binding and transfer of heme in bacterial heme-acquisition systems.,Naoe Y, Nakamura N, Rahman MM, Tosha T, Nagatoishi S, Tsumoto K, Shiro Y, Sugimoto H Proteins. 2017 Sep 14. doi: 10.1002/prot.25386. PMID:28913898<ref>PMID:28913898</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5y89" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Burcj]]
+[[Category: Burkholderia cenocepacia J2315]]
-[[Category: Nakamura, N]]
+[[Category: Large Structures]]
-[[Category: Naoe, Y]]
+[[Category: Nakamura N]]
-[[Category: Rahman, M M]]
+[[Category: Naoe Y]]
-[[Category: Shiro, Y]]
+[[Category: Rahman MM]]
-[[Category: Sugimoto, H]]
+[[Category: Shiro Y]]
-[[Category: Metal transport]]
+[[Category: Sugimoto H]]
-[[Category: Transport protein]]