3ng6: Difference between revisions
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[[Image: | ==The crystal structure of hemoglobin I from Trematomus newnesi in deoxygenated state obtained through an oxidation/reduction cycle in which potassium hexacyanoferrate and sodium dithionite were alternatively added== | ||
<StructureSection load='3ng6' size='340' side='right' caption='[[3ng6]], [[Resolution|resolution]] 2.20Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3ng6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trematomus_newnesi Trematomus newnesi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NG6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NG6 FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr> | |||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3nfe|3nfe]], [[1t1n|1t1n]], [[3d1k|3d1k]], [[2aa1|2aa1]], [[1la6|1la6]]</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=3ng6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ng6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ng6 RCSB], [http://www.ebi.ac.uk/pdbsum/3ng6 PDBsum]</span></td></tr> | |||
</table> | |||
== 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/ng/3ng6_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/chain_selection.php?pdb_ID=2ata ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The Root effect is a widespread property among fish hemoglobins whose structural basis remains largely obscure. Here we report a crystallographic and spectroscopic characterization of the non-Root-effect hemoglobin isolated from the Antarctic fish Trematomus newnesi in its deoxygenated form. The crystal structure unveils that the T state of this hemoglobin is stabilized by a strong H-bond between the side chains of Asp95alpha and Asp101beta at the alpha2beta1 and alpha1beta2 interfaces. This unexpected finding undermines the accepted paradigm that correlates the presence of this unusual H-bond with the occurrence of the Root effect. Surprisingly, the T state is characterized by an atypical flexibility of two alpha chains within the tetramer. Indeed, regions such as the CDalpha corner and the EFalpha pocket, which are normally well ordered in the T state of tetrameric hemoglobins, display high B-factors and non-continuous electron densities. This flexibility also leads to unusual distances between the heme iron and the proximal and distal His residues. These observations are in line with Raman micro-spectroscopy studies carried out both in solution and in the crystal state. The findings here presented suggest that in fish hemoglobins the Root effect may be switched off through a significant destabilization of the T state regardless of the presence of the inter-aspartic H-bond. Similar mechanisms may also operate for other non-Root effect hemoglobins. The implications of the flexibility of the CDalpha corner for the mechanism of the T-R transition in tetrameric hemoglobins are also discussed. | |||
An order-disorder transition plays a role in switching off the Root effect in fish hemoglobins.,Vergara A, Vitagliano L, Merlino A, Sica F, Marino K, Verde C, di Prisco G, Mazzarella L J Biol Chem. 2010 Jul 7. PMID:20610398<ref>PMID:20610398</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
==See Also== | ==See Also== | ||
*[[Hemoglobin|Hemoglobin]] | *[[Hemoglobin 3D structures|Hemoglobin 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Trematomus newnesi]] | [[Category: Trematomus newnesi]] | ||
[[Category: Marino, K | [[Category: Marino, K]] | ||
[[Category: Mazzarella, L | [[Category: Mazzarella, L]] | ||
[[Category: Merlino, A | [[Category: Merlino, A]] | ||
[[Category: Sica, F | [[Category: Sica, F]] | ||
[[Category: Vergara, A | [[Category: Vergara, A]] | ||
[[Category: Vitagliano, L | [[Category: Vitagliano, L]] | ||
[[Category: Antarctic fish]] | [[Category: Antarctic fish]] | ||
[[Category: Fish hemoglobin]] | [[Category: Fish hemoglobin]] | ||
[[Category: Oxygen transport]] | [[Category: Oxygen transport]] | ||
[[Category: Root effect]] | [[Category: Root effect]] | ||
Revision as of 16:50, 9 December 2014
The crystal structure of hemoglobin I from Trematomus newnesi in deoxygenated state obtained through an oxidation/reduction cycle in which potassium hexacyanoferrate and sodium dithionite were alternatively addedThe crystal structure of hemoglobin I from Trematomus newnesi in deoxygenated state obtained through an oxidation/reduction cycle in which potassium hexacyanoferrate and sodium dithionite were alternatively added
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe Root effect is a widespread property among fish hemoglobins whose structural basis remains largely obscure. Here we report a crystallographic and spectroscopic characterization of the non-Root-effect hemoglobin isolated from the Antarctic fish Trematomus newnesi in its deoxygenated form. The crystal structure unveils that the T state of this hemoglobin is stabilized by a strong H-bond between the side chains of Asp95alpha and Asp101beta at the alpha2beta1 and alpha1beta2 interfaces. This unexpected finding undermines the accepted paradigm that correlates the presence of this unusual H-bond with the occurrence of the Root effect. Surprisingly, the T state is characterized by an atypical flexibility of two alpha chains within the tetramer. Indeed, regions such as the CDalpha corner and the EFalpha pocket, which are normally well ordered in the T state of tetrameric hemoglobins, display high B-factors and non-continuous electron densities. This flexibility also leads to unusual distances between the heme iron and the proximal and distal His residues. These observations are in line with Raman micro-spectroscopy studies carried out both in solution and in the crystal state. The findings here presented suggest that in fish hemoglobins the Root effect may be switched off through a significant destabilization of the T state regardless of the presence of the inter-aspartic H-bond. Similar mechanisms may also operate for other non-Root effect hemoglobins. The implications of the flexibility of the CDalpha corner for the mechanism of the T-R transition in tetrameric hemoglobins are also discussed. An order-disorder transition plays a role in switching off the Root effect in fish hemoglobins.,Vergara A, Vitagliano L, Merlino A, Sica F, Marino K, Verde C, di Prisco G, Mazzarella L J Biol Chem. 2010 Jul 7. PMID:20610398[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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