2hz2: Difference between revisions

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-[[Image:2hz2.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2hz2", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_2hz2|  PDB=2hz2  |  SCENE=  }}
-'''The x-ray crystal structure of ferric Synechocystis hemoglobin H117A mutant with a covalent linkage'''
+==The x-ray crystal structure of ferric Synechocystis hemoglobin H117A mutant with a covalent linkage==
+<StructureSection load='2hz2' size='340' side='right'caption='[[2hz2]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2hz2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803 Synechocystis sp. PCC 6803]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HZ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HZ2 FirstGlance]. <br>
+</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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</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'>[https://proteopedia.org/fgij/fg.htm?mol=2hz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hz2 OCA], [https://pdbe.org/2hz2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hz2 RCSB], [https://www.ebi.ac.uk/pdbsum/2hz2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hz2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TRHBN_SYNY3 TRHBN_SYNY3] Forms a very stable complex with oxygen. The oxygen dissociation rate is 0.011 s(-1).
+== 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/hz/2hz2_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=2hz2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Synechocystis hemoglobin contains an unprecedented covalent bond between a nonaxial histidine side chain (H117) and the heme 2-vinyl. This bond has been previously shown to stabilize the ferric protein against denaturation, and also to affect the kinetics of cyanide association. However, it is unclear why Synechocystis hemoglobin would require the additional degree of stabilization accompanying the His117-heme 2-vinyl bond because it also displays endogenous bis-histidyl axial heme coordination, which should greatly assist heme retention. Furthermore, the mechanism by which the His117-heme 2-vinyl bond affects ligand binding has not been reported, nor has any investigation of the role of this bond on the structure and function of the protein in the ferrous oxidation state. Here we report an investigation of the role of the Synechocystis hemoglobin His117-heme 2-vinyl bond on structure, heme coordination, exogenous ligand binding, and stability in both the ferrous and ferric oxidation states. Our results reveal that hexacoordinate Synechocystis hemoglobin lacking this bond is less stable in the ferrous oxidation state than the ferric, which is surprising in light of our understanding of pentacoordinate Hb stability, in which the ferric protein is always less stable. It is also demonstrated that removal of the His117-heme 2-vinyl bond increases the affinity constant for intramolecular histidine coordination in the ferric oxidation state, thus presenting greater competition for the ligand binding site and lowering the observed rate and affinity constants for exogenous ligands.
-==Overview==
+Covalent heme attachment in Synechocystis hemoglobin is required to prevent ferrous heme dissociation.,Hoy JA, Smagghe BJ, Halder P, Hargrove MS Protein Sci. 2007 Feb;16(2):250-60. PMID:17242429<ref>PMID:17242429</ref>
-Synechocystis hemoglobin contains an unprecedented covalent bond between a nonaxial histidine side chain (H117) and the heme 2-vinyl. This bond has been previously shown to stabilize the ferric protein against denaturation, and also to affect the kinetics of cyanide association. However, it is unclear why Synechocystis hemoglobin would require the additional degree of stabilization accompanying the His117-heme 2-vinyl bond because it also displays endogenous bis-histidyl axial heme coordination, which should greatly assist heme retention. Furthermore, the mechanism by which the His117-heme 2-vinyl bond affects ligand binding has not been reported, nor has any investigation of the role of this bond on the structure and function of the protein in the ferrous oxidation state. Here we report an investigation of the role of the Synechocystis hemoglobin His117-heme 2-vinyl bond on structure, heme coordination, exogenous ligand binding, and stability in both the ferrous and ferric oxidation states. Our results reveal that hexacoordinate Synechocystis hemoglobin lacking this bond is less stable in the ferrous oxidation state than the ferric, which is surprising in light of our understanding of pentacoordinate Hb stability, in which the ferric protein is always less stable. It is also demonstrated that removal of the His117-heme 2-vinyl bond increases the affinity constant for intramolecular histidine coordination in the ferric oxidation state, thus presenting greater competition for the ligand binding site and lowering the observed rate and affinity constants for exogenous ligands.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-HZ2 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Synechocystis_sp. Synechocystis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HZ2 OCA].
+</div>
+<div class="pdbe-citations 2hz2" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Covalent heme attachment in Synechocystis hemoglobin is required to prevent ferrous heme dissociation., Hoy JA, Smagghe BJ, Halder P, Hargrove MS, Protein Sci. 2007 Feb;16(2):250-60. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17242429 17242429]
+*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
-[[Category: Single protein]]
+== References ==
-[[Category: Synechocystis sp.]]
+<references/>
-[[Category: Hoy, J A.]]
+__TOC__
-[[Category: Covalent heme vinyl link]]
+</StructureSection>
-[[Category: Ferric]]
+[[Category: Large Structures]]
-[[Category: Globin]]
+[[Category: Synechocystis sp. PCC 6803]]
-[[Category: Heme]]
+[[Category: Hoy JA]]
-[[Category: Hemoglobin]]
-[[Category: Hexacoordinate]]
-[[Category: Synechocysti]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 06:53:08 2008''