5y89: Difference between revisions

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==Periplasmic heme-binding protein BhuT in complex with one heme (holo-1)==
==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 ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5y89]] is a 2 chain structure. 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='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>
<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>
</table>
</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__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Nakamura, N]]
[[Category: Burkholderia cenocepacia J2315]]
[[Category: Naoe, Y]]
[[Category: Large Structures]]
[[Category: Rahman, M M]]
[[Category: Nakamura N]]
[[Category: Shiro, Y]]
[[Category: Naoe Y]]
[[Category: Sugimoto, H]]
[[Category: Rahman MM]]
[[Category: Metal transport]]
[[Category: Shiro Y]]
[[Category: Transport protein]]
[[Category: Sugimoto H]]

Latest revision as of 13:22, 27 March 2024

Periplasmic heme-binding protein BhuT in complex with one heme (holo-1)Periplasmic heme-binding protein BhuT in complex with one heme (holo-1)

Structural highlights

5y89 is a 2 chain structure with sequence from Burkholderia cenocepacia J2315. This structure supersedes the now removed PDB entry 5gj0. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

B4EKB3_BURCJ

5y89, resolution 2.40Å

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OCA
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