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| | ==Structure of the partially unliganded met state of 400 kDa hemoglobin: Insights into ligand-induced structural changes of giant hemoglobins== | | ==Structure of the partially unliganded met state of 400 kDa hemoglobin: Insights into ligand-induced structural changes of giant hemoglobins== |
| - | <StructureSection load='2zfo' size='340' side='right' caption='[[2zfo]], [[Resolution|resolution]] 1.95Å' scene=''> | + | <StructureSection load='2zfo' size='340' side='right'caption='[[2zfo]], [[Resolution|resolution]] 1.95Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2zfo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Oligobrachia_mashikoi Oligobrachia mashikoi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZFO FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2zfo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Oligobrachia_mashikoi Oligobrachia mashikoi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZFO FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2d2m|2d2m]], [[2d2n|2d2n]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></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=2zfo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zfo OCA], [http://pdbe.org/2zfo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zfo RCSB], [http://www.ebi.ac.uk/pdbsum/2zfo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zfo ProSAT]</span></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=2zfo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zfo OCA], [https://pdbe.org/2zfo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zfo RCSB], [https://www.ebi.ac.uk/pdbsum/2zfo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zfo ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/GLBB1_OLIMA GLBB1_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and sulfide simultaneously and reversibly at two different sites. [[http://www.uniprot.org/uniprot/GLBA1_OLIMA GLBA1_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites. [[http://www.uniprot.org/uniprot/GLBB2_OLIMA GLBB2_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites. [[http://www.uniprot.org/uniprot/GLBA2_OLIMA GLBA2_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites. | + | [https://www.uniprot.org/uniprot/GLBA1_OLIMA GLBA1_OLIMA] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zf/2zfo_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zf/2zfo_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Oligobrachia mashikoi]] | | [[Category: Oligobrachia mashikoi]] |
| - | [[Category: Fukumori, Y]] | + | [[Category: Fukumori Y]] |
| - | [[Category: Kita, A]] | + | [[Category: Kita A]] |
| - | [[Category: Miki, K]] | + | [[Category: Miki K]] |
| - | [[Category: Nakagawa, T]] | + | [[Category: Nakagawa T]] |
| - | [[Category: Numoto, N]] | + | [[Category: Numoto N]] |
| - | [[Category: Sasayama, Y]] | + | [[Category: Sasayama Y]] |
| - | [[Category: Annelida]]
| + | |
| - | [[Category: Heme]]
| + | |
| - | [[Category: Hemoglobin]]
| + | |
| - | [[Category: Iron]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Oxygen binding]]
| + | |
| - | [[Category: Oxygen transport]]
| + | |
| - | [[Category: Polychaete]]
| + | |
| - | [[Category: Secreted]]
| + | |
| - | [[Category: Transport]]
| + | |
| - | [[Category: Transport protein]]
| + | |
| - | [[Category: Unliganded]]
| + | |
| Structural highlights
Function
GLBA1_OLIMA The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites.
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 PubMed
Recent crystallographic studies have revealed the structures of some invertebrate extracellular giant hemoglobins of 3,600 kDa or 400 kDa and their common quaternary structure of dodecameric subassembly composed of four kinds of globin subunits (A1, A2, B1, and B2). These results have provided insight into the mechanisms of their unique functional properties of oxygen binding and sulfide binding. All of these structures were solved with oxygenated or CO-liganded forms at low or moderate resolutions. We have determined the crystal structure of 400 kDa Hb from a polychaete Oligobrachia mashikoi at 1.95 A resolution. The electron densities at higher resolution confirm the existence of an isoform of the B1 subunit because of the inconsistency with the model that was built from the formerly known amino acid sequence. The brownish color of the crystals used in this study and the absorption spectrum from the dissolved crystals strongly indicated that the obtained structure was a ferric met state, whereas completele absence of electron density around the distal heme pockets were observed at the A2, B1, and B2 subunits. We concluded that the obtained structure was in unliganded met forms at three of four globin subunits in the 24mer assembly and in oxygenated forms at the remaining A1 subunits. The partially unliganded structure showed remarkable structural changes at the AB loop regions causing quaternary rearrangements of the EF-dimer structure. In contrast, few changes occurred at the interface regions composed of the E and F helices. These results suggest that the ligand-induced structural changes of Oligobrachia Hb are quite different from those of the well-studied mollusk Hb having the same EF-dimer structure. The structural rearrangements make the dodecameric subassembliy form a tighter conformation than those of fully oxygenated or CO-liganded dodecamer structure. Proteins 2008. (c) 2008 Wiley-Liss, Inc.
Structure of the partially unliganded met state of 400 kDa hemoglobin: Insights into ligand-induced structural changes of giant hemoglobins.,Numoto N, Nakagawa T, Kita A, Sasayama Y, Fukumori Y, Miki K Proteins. 2008 Apr 8;. PMID:18398907[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Numoto N, Nakagawa T, Kita A, Sasayama Y, Fukumori Y, Miki K. Structure of the partially unliganded met state of 400 kDa hemoglobin: Insights into ligand-induced structural changes of giant hemoglobins. Proteins. 2008 Apr 8;. PMID:18398907 doi:10.1002/prot.22040
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