1v4x: Difference between revisions
No edit summary |
No edit summary |
||
| (9 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Crystal structure of bluefin tuna hemoglobin deoxy form at pH5.0== | |||
<StructureSection load='1v4x' size='340' side='right'caption='[[1v4x]], [[Resolution|resolution]] 1.60Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1v4x]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thunnus_thynnus Thunnus thynnus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V4X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V4X 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]] 1.6Å</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=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=1v4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v4x OCA], [https://pdbe.org/1v4x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v4x RCSB], [https://www.ebi.ac.uk/pdbsum/1v4x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v4x ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q8AYM0_THUTH Q8AYM0_THUTH] | |||
== 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/v4/1v4x_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=1v4x ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The crystal structure of hemoglobin has been known for several decades, yet various features of the molecule remain unexplained or controversial. Several animal hemoglobins have properties that cannot be readily explained in terms of their amino acid sequence and known atomic models of hemoglobin. Among these, fish hemoglobins are well known for their widely varying interactions with heterotropic effector molecules and pH sensitivity. Some fish hemoglobins are almost completely insensitive to pH (within physiological limits), whereas others show extremely low oxygen affinity under acid conditions, a phenomenon called the Root effect. X-ray crystal structures of Root effect hemoglobins have not, to date, provided convincing explanations of this effect. Sequence alignments have signally failed to pinpoint the residues involved, and site-directed mutagenesis has not yielded a human hemoglobin variant with this property. We have solved the crystal structure of tuna hemoglobin in the deoxy form at low and moderate pH and in the presence of carbon monoxide at high pH. A comparison of these models shows clear evidence for novel mechanisms of pH-dependent control of ligand affinity. | |||
Novel mechanisms of pH sensitivity in tuna hemoglobin: a structural explanation of the root effect.,Yokoyama T, Chong KT, Miyazaki G, Morimoto H, Shih DT, Unzai S, Tame JR, Park SY J Biol Chem. 2004 Jul 2;279(27):28632-40. Epub 2004 Apr 26. PMID:15117955<ref>PMID:15117955</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1v4x" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Hemoglobin|Hemoglobin]] | *[[Hemoglobin 3D structures|Hemoglobin 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Thunnus thynnus]] | [[Category: Thunnus thynnus]] | ||
[[Category: Chong | [[Category: Chong KT]] | ||
[[Category: Jeremy | [[Category: Jeremy RHT]] | ||
[[Category: Miyazaki | [[Category: Miyazaki G]] | ||
[[Category: Miyazaki | [[Category: Miyazaki Y]] | ||
[[Category: Morimoto | [[Category: Morimoto H]] | ||
[[Category: Nakatsukasa | [[Category: Nakatsukasa T]] | ||
[[Category: Park | [[Category: Park SY]] | ||
[[Category: Unzai | [[Category: Unzai S]] | ||
[[Category: Yokoyama | [[Category: Yokoyama T]] | ||
Latest revision as of 02:57, 28 December 2023
Crystal structure of bluefin tuna hemoglobin deoxy form at pH5.0Crystal structure of bluefin tuna hemoglobin deoxy form at pH5.0
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 PubMedThe crystal structure of hemoglobin has been known for several decades, yet various features of the molecule remain unexplained or controversial. Several animal hemoglobins have properties that cannot be readily explained in terms of their amino acid sequence and known atomic models of hemoglobin. Among these, fish hemoglobins are well known for their widely varying interactions with heterotropic effector molecules and pH sensitivity. Some fish hemoglobins are almost completely insensitive to pH (within physiological limits), whereas others show extremely low oxygen affinity under acid conditions, a phenomenon called the Root effect. X-ray crystal structures of Root effect hemoglobins have not, to date, provided convincing explanations of this effect. Sequence alignments have signally failed to pinpoint the residues involved, and site-directed mutagenesis has not yielded a human hemoglobin variant with this property. We have solved the crystal structure of tuna hemoglobin in the deoxy form at low and moderate pH and in the presence of carbon monoxide at high pH. A comparison of these models shows clear evidence for novel mechanisms of pH-dependent control of ligand affinity. Novel mechanisms of pH sensitivity in tuna hemoglobin: a structural explanation of the root effect.,Yokoyama T, Chong KT, Miyazaki G, Morimoto H, Shih DT, Unzai S, Tame JR, Park SY J Biol Chem. 2004 Jul 2;279(27):28632-40. Epub 2004 Apr 26. PMID:15117955[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||