3d1k: Difference between revisions
New page: '''Unreleased structure''' The entry 3d1k is ON HOLD Authors: Vitagliano, L., Vergara, A., Bonomi, G., Merlino, A., Mazzarella, L. Description: R/T intermediate quaternary structure of... |
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The | ==R/T intermediate quaternary structure of an antarctic fish hemoglobin in an alpha(CO)-beta(pentacoordinate) state== | ||
<StructureSection load='3d1k' size='340' side='right'caption='[[3d1k]], [[Resolution|resolution]] 1.25Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3d1k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trematomus_newnesi Trematomus newnesi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D1K 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]] 1.25Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <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=3d1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d1k OCA], [https://pdbe.org/3d1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d1k RCSB], [https://www.ebi.ac.uk/pdbsum/3d1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d1k ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/HBA1_TRENE HBA1_TRENE] | |||
== 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/d1/3d1k_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=3d1k ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Tetrameric hemoglobins represent the most commonly used model for the description of the basic concepts of protein allostery. The classical stereochemical model assumes a concerted transition of the protein, upon oxygen release, from the relaxed (R) to the tense (T) state. Despite the large amount of data accumulated on the end-points of the transition, scarce structural information is available on the intermediate species along the pathway. Here we report a spectroscopic characterization of the autoxidation process of the Trematomus newnesi major Hb component and the atomic resolution structure (1.25 A) of an intermediate form along the pathway characterized by a different binding and oxidation state of the alpha and beta chains. In contrast to the alpha-heme iron, which binds a CO molecule, the beta iron displays a pentacoordinated oxidized state, which is rare in tetrameric hemoglobins. Interestingly, the information provided by the present analysis is not limited to the characterization of the peculiar oxidation process of Antarctic fish hemoglobins. Indeed, this structure represents the most detailed snapshot of hemoglobin allosteric transition hitherto achieved. Upon ligand release at the beta heme, a cascade of structural events is observed. Notably, several structural features of the tertiary structure of the alpha and beta chains closely resemble those typically observed in the deoxygenated state. The overall quaternary structure also becomes intermediate between the R and the T state. The analysis of the alterations induced by the ligand release provides a clear picture of the temporal sequence of the events associated with the transition. The implications of the present findings have also been discussed in the wider context of tetrameric Hbs. | |||
Spectroscopic and Crystallographic Characterization of a Tetrameric Hemoglobin Oxidation Reveals Structural Features of the Functional Intermediate Relaxed/Tense State.,Vitagliano L, Vergara A, Bonomi G, Merlino A, Verde C, Prisco GD, Howes BD, Smulevich G, Mazzarella L J Am Chem Soc. 2008 Jul 22. PMID:18642904<ref>PMID:18642904</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3d1k" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Hemoglobin 3D structures|Hemoglobin 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Trematomus newnesi]] | |||
[[Category: Bonomi G]] | |||
[[Category: Mazzarella L]] | |||
[[Category: Merlino A]] | |||
[[Category: Vergara A]] | |||
[[Category: Vitagliano L]] | |||
Latest revision as of 15:37, 30 August 2023
R/T intermediate quaternary structure of an antarctic fish hemoglobin in an alpha(CO)-beta(pentacoordinate) stateR/T intermediate quaternary structure of an antarctic fish hemoglobin in an alpha(CO)-beta(pentacoordinate) state
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedTetrameric hemoglobins represent the most commonly used model for the description of the basic concepts of protein allostery. The classical stereochemical model assumes a concerted transition of the protein, upon oxygen release, from the relaxed (R) to the tense (T) state. Despite the large amount of data accumulated on the end-points of the transition, scarce structural information is available on the intermediate species along the pathway. Here we report a spectroscopic characterization of the autoxidation process of the Trematomus newnesi major Hb component and the atomic resolution structure (1.25 A) of an intermediate form along the pathway characterized by a different binding and oxidation state of the alpha and beta chains. In contrast to the alpha-heme iron, which binds a CO molecule, the beta iron displays a pentacoordinated oxidized state, which is rare in tetrameric hemoglobins. Interestingly, the information provided by the present analysis is not limited to the characterization of the peculiar oxidation process of Antarctic fish hemoglobins. Indeed, this structure represents the most detailed snapshot of hemoglobin allosteric transition hitherto achieved. Upon ligand release at the beta heme, a cascade of structural events is observed. Notably, several structural features of the tertiary structure of the alpha and beta chains closely resemble those typically observed in the deoxygenated state. The overall quaternary structure also becomes intermediate between the R and the T state. The analysis of the alterations induced by the ligand release provides a clear picture of the temporal sequence of the events associated with the transition. The implications of the present findings have also been discussed in the wider context of tetrameric Hbs. Spectroscopic and Crystallographic Characterization of a Tetrameric Hemoglobin Oxidation Reveals Structural Features of the Functional Intermediate Relaxed/Tense State.,Vitagliano L, Vergara A, Bonomi G, Merlino A, Verde C, Prisco GD, Howes BD, Smulevich G, Mazzarella L J Am Chem Soc. 2008 Jul 22. PMID:18642904[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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