2z6f: Difference between revisions

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-{{Seed}}
-[[Image:2z6f.png|left|200px]]
-<!--
+==Crystal structure of NEAT domain from Staphylococcus aureus in complex with heme==
-The line below this paragraph, containing "STRUCTURE_2z6f", creates the "Structure Box" on the page.
+<StructureSection load='2z6f' size='340' side='right'caption='[[2z6f]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2z6f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_Mu50 Staphylococcus aureus subsp. aureus Mu50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z6F FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</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>
-{{STRUCTURE_2z6f|  PDB=2z6f  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2z6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z6f OCA], [https://pdbe.org/2z6f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z6f RCSB], [https://www.ebi.ac.uk/pdbsum/2z6f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z6f ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ISDH_STAAM ISDH_STAAM] Binds human plasma haptoglobin-hemoglobin complexes, haptoglobin and hemoglobin. Binds haptoglobin-hemoglobin complexes with significantly higher affinity than haptoglobin alone (By similarity).
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z6/2z6f_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2z6f ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+To elucidate the heme acquisition system in pathogenic bacteria, we investigated the heme-binding properties of the third NEAT domain of IsdH (IsdH-NEAT3), a receptor for heme located on the surfaces of pathogenic bacterial cells, by using x-ray crystallography, isothermal titration calorimetry, examination of absorbance spectra, mutation analysis, size-exclusion chromatography, and analytical ultracentrifugation. We found the following: 1) IsdH-NEAT3 can bind with multiple heme molecules by two modes; 2) heme was bound at the surface of IsdH-NEAT3; 3) candidate residues proposed from the crystal structure were not essential for binding with heme; and 4) IsdH-NEAT3 was associated into a multimeric heme complex by the addition of excess heme. From these observations, we propose a heme-binding mechanism for IsdH-NEAT3 that involves multimerization and discuss the biological importance of this mechanism.
-===Crystal structure of NEAT domain from Staphylococcus aureus in complex with heme===
+Structural basis for multimeric heme complexation through a specific protein-heme interaction: the case of the third neat domain of IsdH from Staphylococcus aureus.,Watanabe M, Tanaka Y, Suenaga A, Kuroda M, Yao M, Watanabe N, Arisaka F, Ohta T, Tanaka I, Tsumoto K J Biol Chem. 2008 Oct 17;283(42):28649-59. Epub 2008 Jul 30. PMID:18667422<ref>PMID:18667422</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2z6f" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18667422}}, adds the Publication Abstract to the page
+*[[Haptoglobin receptor|Haptoglobin receptor]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18667422 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18667422}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-Z6F is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6F OCA].
+[[Category: Staphylococcus aureus subsp. aureus Mu50]]
+[[Category: Suenaga A]]
-==Reference==
+[[Category: Tanaka Y]]
-Structural basis for multimeric heme complexation through a specific protein-heme interaction: the case of the third neat domain of IsdH from Staphylococcus aureus., Watanabe M, Tanaka Y, Suenaga A, Kuroda M, Yao M, Watanabe N, Arisaka F, Ohta T, Tanaka I, Tsumoto K, J Biol Chem. 2008 Oct 17;283(42):28649-59. Epub 2008 Jul 30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18667422 18667422]
+[[Category: Tsumoto K]]
-[[Category: Single protein]]
-[[Category: Staphylococcus aureus]]
-[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
-[[Category: Cell wall]]
-[[Category: Heme binding protein]]
-[[Category: Igg-like fold]]
-[[Category: Peptidoglycan-anchor]]
-[[Category: Secreted]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 10 20:30:16 2008''