3nu1: Difference between revisions

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<StructureSection load='3nu1' size='340' side='right'caption='[[3nu1]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
<StructureSection load='3nu1' size='340' side='right'caption='[[3nu1]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3nu1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Yerpa Yerpa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NU1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NU1 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3nu1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pestis_Antiqua Yersinia pestis Antiqua]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NU1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NU1 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 2.5&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HMUT, Y0541, YPA_4001, YPO0281, YP_0436 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=360102 YERPA])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=3nu1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nu1 OCA], [https://pdbe.org/3nu1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nu1 RCSB], [https://www.ebi.ac.uk/pdbsum/3nu1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nu1 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=3nu1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nu1 OCA], [https://pdbe.org/3nu1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nu1 RCSB], [https://www.ebi.ac.uk/pdbsum/3nu1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nu1 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/A0A0E1NWS3_YERPA A0A0E1NWS3_YERPA]
The periplasmic binding protein HmuT from Yersinia pestis (YpHmuT) is a component of the heme uptake locus hmu and delivers bound hemin to the inner-membrane-localized, ATP-binding cassette (ABC) transporter HmuUV for translocation into the cytoplasm. The mechanism of this process, heme transport across the inner membrane of pathogenic bacteria, is currently insufficiently understood at the molecular level. Here we describe the crystal structures of the substrate-free and heme-bound states of YpHmuT, revealing two lobes with a central binding cleft. Superposition of the apo and holo states reveals a minor tilting motion of the lobes surrounding concomitant with heme binding. Unexpectedly, YpHmuT binds two stacked hemes in a central binding cleft that is larger than those of the homologous periplasmic heme-binding proteins ShuT and PhuT, both of which bind only one heme. The hemes bound to YpHmuT are coordinated via a tyrosine side chain that contacts the Fe atom of one heme and a histidine that contacts the Fe atom of the other heme. The coordinating histidine is only conserved in a subset of heme substrate binding proteins, suggesting that its presence predicts the ability to bind two heme molecules simultaneously. The structural data are supported by spectroscopic binding studies performed in solution, where up to two hemes can bind to YpHmuT. Isothermal titration calorimetry suggests that the two hemes are bound in discrete, sequential steps and with dissociation constants (K(D)) of approximately 0.29 and approximately 29 nM, which is similar to the affinities observed in other bacterial substrate binding proteins. Our findings suggest that the cognate ABC transporter HmuUV may simultaneously translocate two hemes per reaction cycle.
 
Two Stacked Heme Molecules in the Binding Pocket of the Periplasmic Heme-Binding Protein HmuT from Yersinia pestis.,Mattle D, Zeltina A, Woo JS, Goetz BA, Locher KP J Mol Biol. 2010 Oct 1. PMID:20888343<ref>PMID:20888343</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3nu1" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Yerpa]]
[[Category: Yersinia pestis Antiqua]]
[[Category: Goetz, B A]]
[[Category: Goetz BA]]
[[Category: Locher, K P]]
[[Category: Locher KP]]
[[Category: Mattle, D]]
[[Category: Mattle D]]
[[Category: Woo, J S]]
[[Category: Woo JS]]
[[Category: Alpha beta protein]]
[[Category: Heme transport]]
[[Category: Iron transport]]
[[Category: Metal transport]]
[[Category: Rigid helical backbone]]
[[Category: Substrate-bound]]
[[Category: Transport protein]]

Latest revision as of 13:01, 14 February 2024

Structure of holo form of a periplasmic heme binding proteinStructure of holo form of a periplasmic heme binding protein

Structural highlights

3nu1 is a 2 chain structure with sequence from Yersinia pestis Antiqua. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A0E1NWS3_YERPA

3nu1, resolution 2.50Å

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